Phonemic spelling turns homophones into homografs: [right, write, rite] become [rait].
In a consistent alphabetical systems, words that rhyme are spelled the same.  If you want to distinguish words with different meanings in writing, then it must be done in speech first. The minor/miner distinction could be retained as mainor/main@r. In speech, there is usually no clear distinction between between unstressed vowels. The issue is whether or not the distinction is important enough to complicate the writing system.  Why should the writing system be any more complicated than the pronunciation guide in a dictionary?
There is always some artistic license.  rait could be spelled wrait and pronounced /werait/. The word may have been pronounced /urait/ at one time just as [knife] was pronounced as spelled before 1400.

Homophones are no more of a problem in writing than they are in speaking.  Usually the context will clearly reveal which meaning or interpretation is appropriate.  Hi pleid in the mainr lieg.  Wi dont sell bier tu mainrz.  Mainrz can no longer bi coal mainrz.

The more serious problem is code overlap [e.g., homographic heterophones].  Some code overlaps are the result of trying to distingiush homophones [such as miner and minor] in writing.  However, most heterographic homophones  are just accidents or unplanned evolutions. 

Code overlaps occur in syllables and vowel spellings as well as in whole words.  The following table shows a range of overlaps for the spelling [ise] which can be interpreted as /is/ /i:s/ /ais/ /aiz/
 

Traditional	promise	paradise	surprise	expertise
Spanglish	prommis	parradais	serpraiz    sapraiz	experties
IPA	'pra:mis	'paer@d@ is	s@ r 'praiz  s'praiz	'eksp@ rti:s
Truespel	praamis praumis	pairudies	serpriez	eksperties
Unifon	promis	paradIs	scrprIz	ekspcrtEs
RITE	promis	paradice	surprise	expertees
Cut Spelling	promis	paradise	surprise	expertise?

.
Promise and paradise and surprise are certainly cases of the same spelling for different sounds, i.e., homographic heterophones.  The phonemic transcriptions are listed above first.  Phonemic systems are logically consistent but do not necessarily look alike.The last two transcriptions, RITE & CS, are 70% solutions.  They are 50% more consistent than TS [traditional spelling] but not systematic or phonemic.

Homophones [same sound] are words that are pronounced alike even if they differ in spelling, meaning, and/or origin: e.g., "pair" and "pear". Homophones may also be spelled alike, as in "bear" (the animal) and "bear" (to carry). These are sometimes called homonyms. The list below, however, consists only of homophones that are not spelled alike [heterographic homophones]. 

Heterograph  [different look] Heterographs are words that are spelled the same but may not be pronounced the same.  Homographs [same appearance on the page]

[BELOW: ambiguous labels with respect to the above]
Homonym  This term sometimes refers to the subset of homophones that are spelled alike [such as the 'bear' example above]  and sometimes  to any homophone such as [pair-pare-pear]. A homonym is usually a homographic homophone but not necessarily.

Synonym [same meaning].  Words that neither look nor sound alike can still mean the same thing [bear-carry]. The meaning dimensioins is absent from the following table.

sight    -/-    sound	homo-phone [same sound]	hetero-phone [different sound]
homo-graph [same look or shape]	ear rhyme = eye rhyme same spelling & sound bear - animal or carry	same spelling different pronunciation tear  /tir/  or  /ter/
hetero-graph [different look or shape]	different spelling -  same pronunciation bare - uncovered homophonic heterograph	different spelling different pronunciation Could have the same meaning - synonym

Code Overlap can refer to identical spellings with two different meanings and pronunciations [homographic heterophones] or to different spellings with the same pronunciation and different meanings [homophonic heterographs]. 

Reply:   As shown above, none of the example words would have to be homophonic homographs.  They could become heterophonic heterographs.  However, the chief advantage of a broad phonemic transcription is to eliminate minor variations in pronunciation and spelling.   To simply spelling it makes sense to merge [mainer-mainor] into mainr or m'ynr. 

Note:  To pronounce mainr pronounce the a as uh or ah, the i as ee in see and ski, and 
the r as er in her. [mainr] = [mah-ee-ner]  In Spanglish, a always = schwa [uh] or an unstressed aa.  y unless followed by a vowel is pronounced as an unstressed /i:/ [very].  [my] would be pronounced as in [tummy]. The pronoun would be spelled mai.

Contrariwise, ambiguous spellings like <bow, close, does, dove, lead, live, minute, number, read, use, wind, wound> currently are a problem; and such misleading homographic heterophones could be sorted out by the most moderate of spelling reforms.  bow/bau [bo/bou], clowz/cloaz/cloas, daz [duzz]/doas/doaz, dav [duvv]/doav, liv/laiv, minnat/mainut, numbr/nummr, ried/read/red, yuus/yuuz, wind/waind, wund/waund.  [for more, go to bad arguments against reform]

The format of the list is as follows. Each set of homophones is on a single line terminated by a return. The members of a set are separated by commas with no trailing spaces. (Thus it is essentially the same as "comma-delimited" database format.) The list is alphabetized by the first word (the headword) in each set (line). Each word in the list occurs as a headword; thus each word occurs at least twice: once as a headword and at least once in the tail of the list. This scheme permits retrieval from the list by examining the headword of each line only. For instance: ascent,assent assent,ascent In general, regularly inflected forms of an entry are not included; thus the list contains "bough, bow" but not "boughs, bows". 

Rhymes with the syllabic n  stubbrn, Mellbrn, Biekn, Cristyn, Cyubn
                             ebon, leben (African curdled milk), gibbon, ribbon, auburn,
                             corban (biblical gift), Bourbon, Oban, stubborn, Cuban,
                             Melbourne, Gisborne (New Zealand port), Lisbon, Brisbane,
                             blacken, slacken, bracken, beckon, Deccan, schnecken 
                             pekan (US mammal), reckon, Brecon, liken,
                             lichen, silken, Vulcan, Lincoln, Duncan, drunken, shrunken,
                             sunken, scutcheon, scuncheon (part of doorjamb),
                             luncheon, puncheon (large cask), truncheon, Christian,
                             Arden, Baden, Dardan (Trojan), garden, harden, lardon
                             (strip of fat), pardon, bourdon (organ stop), hoyden
                             (tomboy), Croydon, loden (thick wool), Snowdon, Woden
                             (Anglo-Saxon god), louden, sudden, wooden, Camden,
                             tendon, linden, Swindon, bounden, London, Hampden,
                             Dresden, deafen, hyphen, siphon, often, soften, orphan,
                             roughen, druffen (Dialect drunk), toughen, lagan
                             (wreckage on sea bed), Skagen (cape in Denmark), Dagan
                             (Babylonian god), jargon, Hagen (German legendary
                             character), Keegan, vegan, tigon (tiger-lion hybrid), bogan
                             (Canadian side stream), hogan (American Indian dwelling),
                             Logan, slogan, brogan (heavy boot), roentgen, largen,
                             Georgian, Trojan, Belgian, Injun, St. John, dungeon, Allen,
                             Alan, gallon, talon, Galen (Greek physician), merlon (part
                             of battlement), pylon, fallen, courlan (US wading bird),
                             sullen, woollen, raglan, barman, carman, Raman (Indian
                             physicist), Brahman, Emmen (Dutch city), lemon, German,
                             Herman, merman, sermon, Sherman, pieman, Simon,
                             Cimon (Athenian military commander), fireman, wireman
                             (US electrician), common, doorman, foreman, lawman,
                             Mormon, Norman, bowman (oarsman), cowman,
                             ploughman, summon, cabman, kirkman (Scot church
                             member), workman, socman (tenant farmer), stockman,
                             milkman, linkman, churchman, Scotchman, watchman,
                             coachman, Dutchman, henchman, Frenchman, adman,
                             badman, madman, Bradman (Australian cricketer),
                             headman, birdman, freedman, goodman, woodman,
                             sandman, bagman (travelling salesman), flagman, ragman,
                             swagman, legman (US newspaper reporter), tegmen
                             (insect's leathery forewing), Bergman, dogman (Austral
                             crane-driver's assistant), frogman, dolman (long Turkish
                             robe), coalman, oilman, Pullman, penman, gunman,
                             hangman, strongman, apeman, Helpmann (Australian ballet
                             dancer), gasman, baseman (fielder in baseball), spaceman,
                             horseman, Norseman, houseman, batsman, statesman,
                             Scotsman, yachtsman, sportsman, craftsman,
                             draughtsman, huntsman, freshman, bushman, Welshman,
                             batman, atman (Hindu self), hetman (Cossack leader),
                             Pitman, pitman, titman (smallest piglet in litter), Whitman
                             (US poet), boatman, footman, postman, dustman,
                             caveman, marksman, spokesman, Manxman, Tasman,
                             Osman (Turkish sultan), oarsman, tribesman, guardsman,
                             tradesman, herdsman, sidesman (church warden's
                             assistant), swordsman, bandsman, landsman, roundsman,
                             groundsman, bailsman (person who stands bail), dalesman,
                             salesman, clansman, Klansman (Ku Klux Klan member),
                             kinsman, linesman, townsman, Canaan, Lennon, pennon,
                             tenon, happen, sharpen, tarpon (Atlantic fish), weapon,
                             cheapen, deepen, steepen, Ripon, Crippen, ripen, open,
                             dampen, lampern (European lamprey), crampon, hempen,
                             tympan (resonating membrane), lumpen (stupid), aspen,
                             saucepan, Aran, Arran, barren, baron, Karen, marron
                             (chestnut), Sharon, heron, perron (flight of steps), Aaron,
                             Charon (Greek mythological character), sporran, warren,
                             squadron, children, cauldron, chaldron (unit of capacity),
                             pauldron (armour plate protecting shoulder), saffron,
                             apron, matron, natron (a mineral), patron, citron,
                             plectron, chevron, sovran, bison, hyson (Chinese green
                             tea), grison (predatory mammal), coarsen, Dawson,
                             whoreson, hoarsen, Porson (English classical scholar),
                             moisten, Preussen (German name for Prussia), boatswain,
                             bosun, loosen, Ibsen, Gibson, Hudson, Belsen, kelson
                             (strengthening beam on keel), Nelson, telson (zoology
                             term), Wilson, Samson, Jansen, Nansen, Johnson, sponson
                             (ship's outboard gun platform), Bunsen, Simpson,
                             Thompson, stetson, Whitsun, Watson, tutsan (Eurasian
                             woodland shrub), Martian, cushion, auction, sanction,
                             sponsion (sponsorship), Dayton (US city), phaeton
                             (horse-drawn carriage), straighten, straiten (embarrass
                             financially), Satan, oaten (made of oats), croton (tropical
                             shrub), Acton, Clacton, lectern, Stockton, plankton,
                             chieftain, Carlton, Charlton, Chiltern, Milton, Stilton,
                             Wilton, Dalton (English scientist), saltern (salt works),
                             Walton, Bolton, molten, sultan, Danton (French
                             revolutionary leader), lantern, Scranton (Pennsylvanian
                             city), Paignton, Denton (English town), lenten, Trenton (US
                             city), wanton, Taunton, hapten (medical term), Clapton
                             (English rock guitarist), Skipton, Hampton, Aston, pastern,
                             eastern, Boston, postern, pleuston (mass of floating
                             microorganisms), Houston, Gladstone, Maidstone,
                             charleston, Princeton, Dunstan (English saint), tungsten,
                             capstan, Ashton, Caxton, Paxton (English architect),
                             sexton (church caretaker), Folkestone, Buxton, Nathan,
                             earthen, python, luthern (dormer window), lengthen,
                             strengthen, heathen, northern, southern, smoothen,
                             cavern, raven (seize prey), tavern, proven, sylvan (relating
                             to woods), Malvern, seawan (shell beads), Jackson, klaxon,
                             flaxen, Saxon, waxen, Texan, Nixon, vixen, oxen, Oxon>,
                             coxswain, bullion, Julian, onion, bunion, Bunyan, Runyon
                             (US writer), grunion (Californian fish), trunnion (pivot),
                             Tarzan, cousin, cozen (to trick), dozen, damson, crimson.

                             Labuan (Malaysian island), DonJuan, Moroccan, Monacan,
                             Faliscan (ancient Italian language), Franciscan,
                             escutcheon, unchristian, exhaustion, combustion, Basildon,
                             Wimbledon, abandon, Ugandan, Clarendon, Abingdon,
                             Hillingdon, Huntingdon, toboggan, Aragon, paragon,
                             tarragon, suffragan (assistant bishop), martagon (Eurasian
                             lily), Monaghan (Irish county), downfallen (dilapidated),
                             chapfallen (dejected), crestfallen, gonfalon (banner),
                             mamelon (small rounded hillock), ortolan (small bird),
                             biathlon, decathlon, pentathlon, uncommon, discommon
                             (legal term), Roscommon (Irish county), husbandman,
                             Orangeman, patrolman, stableman, nobleman, middleman,
                             rifleman, signalman, muscleman, cattleman, gentleman,
                             midshipman, policeman, businessman, serviceman,
                             warehouseman, Englishman, Irishman, aircraftman,
                             merchantman (merchant ship), harvestman (arachnid),
                             talisman, exciseman, ombudsman, backwoodsman,
                             Lebanon, reopen, half-open, Saharan, Anderson, Jefferson,
                             Emerson, Saracen, Paterson, Peterson, Richardson,
                             Nicholson, Mendelssohn, Williamson, Robinson, Dickinson,
                             Atkinson, Stephenson, pincushion, infarction, decoction
                             (medicinal preparation), concoction, intinction (part of
                             Communion), distinction, extinction, emulsion, repulsion,
                             propulsion, impulsion, compulsion, expulsion, revulsion,
                             divulsion (tearing apart), avulsion (forcible separation),
                             convulsion, pre-emption, redemption, exemption,
                             occasion, equation, abrasion, pervasion, evasion,
                             invasion, persuasion, dissuasion, quieten, Pinkerton,
                             charlatan, tarlatan (cotton fabric), Sheraton, Chatterton,
                             Chesterton, doubleton (bridge term), subaltern,
                             Shackleton, Middleton, singleton, Hamilton, simpleton,
                             Edmonton, Bebington, Tarkington (US novelist), Arlington
                             (Virginian county), Darlington, Ellington (US jazz musician),
                             Wellington, Burlington, Islington, Leamington, Lymington,
                             Warrington, Accrington, Washington, Whittington,
                             Lexington (US city), Kensington, Northampton,
                             Southampton, Augustan, Palmerston, autochthon (country's
                             earliest-known inhabitant), Carmarthen, cordovan (fine
                             leather), Donovan, Amazon.

                             inescutcheon (heraldic term), Muhammadan, solenodon
                             (shrew-like mammal), Tutankhamen, Landeshauptmann
                             (Austrian state governor), polyhedron, rhombohedron,
                             decahedron, tetrahedron, octahedron, hexahedron,
                             rhododendron, philodendron (climbing plant),
                             hobson-jobson (folk etymology), Wolverhampton,
                             Aldermaston, Saskatchewan, Elizabethan. nation, station.

                             striation, Croatian (language group), libation, vacation,
                             plication (folding), truncation, laudation (praise),
                             foundation, purgation, lallation (speech defect), dilation,
                             collation, ablation, oblation (religious offering), deflation,
                             reflation, stagflation (economics term), inflation,
                             translation, squamation (formation of scales), formation,
                             summation, Dalmatian, planation (erosion of land surface),
                             vernation (leaf arrangement in bud), venation
                             (arrangement of veins), zonation, lunation (lunar month),
                             damnation, crispation (curling), serration, gyration,
                             oration, libration (oscillating), vibration, migration,
                             titration, filtration, castration, prostration, frustration,
                             cassation (legal term), cessation, Alsatian, pulsation,
                             flirtation, fetation (state of pregnancy), citation,
                             dictation, lactation, saltation (biology term), temptation,
                             gustation (tasting), crustacean, substation, outstation,
                             lavation (washing), starvation, nivation (geology term),
                             privation, ovation, novation (legal term), salvation,
                             solvation (chemistry term), fixation, causation.

                             conurbation, incubation, titubation, education, inculcation,
                             coruscation (gleam of light), retardation, denudation,
                             exudation, inundation, subjugation, conjugation,
                             promulgation, elongation, prolongation, insolation
                             (exposure to solar radiation), contemplation, legislation,
                             deformation, preformation, malformation, conformation,
                             exhumation, subornation, indignation, assignation,
                             designation, resignation, condemnation, usurpation,
                             occupation, syncopation, aspiration, inspiration,
                             expiration, lucubration (laborious study), desecration,
                             consecration, dehydration, conflagration, arbitration,
                             penetration, infiltration, concentration, orchestration,
                             sequestration, illustration, demonstration, conversation,
                             deportation, importation, transportation, exportation,
                             exhortation, exploitation, affectation, delectation,
                             expectation, eructation (belching), exaltation, exultation,
                             auscultation, consultation, supplantation, implantation,
                             transplantation, confrontation, presentation, coaptation
                             (reuniting two surfaces), acceptation, adaptation,
                             forestation, devastation, salivation, elevation, derivation,
                             deprivation, titivation, motivation, activation, cultivation,
                             captivation, aestivation (biology term), excavation,
                             renovation, innovation, aggravation, depravation,
                             conservation, reservation, preservation, observation,
                             accusation.

                             coeducation, interlunation (period of moon's invisibility),
                             preoccupation, intermigration, superfetation (medical
                             term), preadaptation (biology term).
 

                             Rhymes for creation

                             radiation, mediation, lineation (outline), expiation,
                             variation, recreation, re-creation, procreation, fasciation
                             (abnormal flattening of stems), aviation.

                             irradiation, repudiation, retaliation, delineation,
                             columniation (arrangement of architectural columns),
                             inebriation, appropriation, repatriation, expatriation,
                             dissociation, association, expatiation, ingratiation,
                             depreciation, appreciation, negotiation, substantiation,
                             asphyxiation.

How the ancient egyptians handled homophones