Question on "weird" native ortography

I'm working on Machichki /ma't͡ʃit͡ʃki/ and recently I'm giving some thought to its writing system. I have some material here on their "knotting", but I'm thinking on how these things translate to writing once government ortography get standardized. Machichki writing system usually represent every consonant in a word, but just the stressed vowel, so: Machichki would be akin to "mchichk" in its writing system (with shenanigans).

My main doubt is: could that survive in a language without any root system? There's some homographs popping up recently, as take and taki and taku (all of them: Tak). I think the government would tend to write with all the vowels to avoid problems, but would that affect society enough? Some things that could be influential on the analysis:

  1. Every nasal vowel is written, but they are mostly stressed.

  2. Vowels are kept when the inflection changes the stresse (take is homograph to taku <tak>, but their plurals aren't: takeki <takek> and takuki <takuk>).

  3. Hiatus can exist, but are indicated clearly (different depending on the vowels involved in it).

  4. Outside of the vowels, the system is pretty much well behaved.

  5. Syllable structure is usually no more than CVC or CV, but there's plenty of words with triconsonantal encounters, usually: CVCC.CV (most common) or CVC.CCV (not very common).

  6. I'm thinking on a highly literate society that had some understanding of the writing pre-standardization but is mostly State-educated after the standardizing effort.