I agree with most details in the two above contributions by @CrazyRocky and @PADev . Still I am seeing a language, where a substantial list of homonyms which are not homophones are not easily understood by the native speakers, because the written representation is not giving them the full information they would get from oral.
This is about short verbs, where diacritics are already in use to show some TAM-information and grammar, so not easily fixed. And the team has got a nice collection of real-life or real-journalism examples where this old myth “the context will always tell” is just not true.
Not true even for the area of nouns, so the population has decided a few years ago from a real need, to mark minimal pairs for nouns and it has proven very helpful for the authors/journalists and for the readers.
Now underlining is indeed tricky and full of technical pitfalls. Luckily there are Unicode diacritics which just look like underlines and which should be treated by most systems like any other ugly or not (combining) diacritics. I am thinking of stuff like U+0332 COMBINING LOW LINE : underline, underscore.
This would be closer to PADev’s advice to “use something in Unicode” and CrazyRocky’s who has also mentioned diacritics. It would just look line underlining. And luckily most websites and apps do no longer use underlining (and bright blue) for links, so in a few years this feature might be liberated for local use. And yes, it can and should be taught locally like any other part of the orthography.
I am not recommending to use this idea without a real study of pros and cons. But I have also learnt that most languages have quirks and “weird details” and that coming in as an outside org to “help and fix” stuff is not always welcome and might also damage the identity or charm of a given languge. Just try to tell the Francophone to get rid of their cedilles for something more mainstream…
Personally I would not enjoy typing or processing entire words which would use the combinging-diacritic-technology on each character to distinguish words from each other. But I believe PT8 has got enough tools (like autocorrect.txt) to potentially handle exotic stuff like this and even publishing in print or modern media should be possible.
So the OP has asked about how to do this potentially. And a forum like this can give input that there might be enough reasons for the owners of that orthography to consider changing it. But that is always emotional and such input should be given with love and with much listening. I would love to hear more from @MSEAIT/LT if and how this detail was handled finally and how it is being received.
Sometimes I see contributions in other fora like “you should not do this, you should not even want this” and often I have a feeling that it means “… because I / we / our_beloved_tool cannot do it”. This is why I added a few words that I believe PT8 can do it, if those concerned want to go ahead this way. fwiw