In order to answer your question properly, one has to go to the etymology of ancestor of Coptic language and the etymology of nouns. Coptic is regarded as the descendant of Egyptian language. Egyptian language in all its 3 scripts, Hieroglyphic, Hieratic and Demotic, was a language that did not only rely on ideograms, but also consonants to express the language. Most words were written only in consonants, the vowels were pronounced but not spelled in most cases for example man was written as rmt, year: rmpt, good: nfrt, heart: ht, woman: shmt, etc. So, we actually do not know exactly how names were pronounced, thus Egyptologists reverted to using the letter e to address the issue e.g. neferet for nfrt however, it could have been nofert, nofart, nafert, nafret, nofrit etc. They had vowels but its usage was relatively less emphasised than consonants. You may want to compare this style of writing to Arabic for example.
Coptic on the contrary comes with a full set of vowels from Greek language, the demotic letters added were all consonants. So, Coptic in a way resembles writing Arabic in English letters aka Arabic Chat Alphabet, Arabizi, Franco etc. There was a lot of inconsistency towards which vowels would represent which sound, which varied between one dialect and the other. Sahidic attempted to minimise differences by the reliance of the supralinear stroke and it was recognised as the formal dialect of Coptic to minimise the idosyncratic usage of vowels across dialects. It was the dialect chosen by St Shenouda Archmandrite for writing instead of the loacl Achmimmic dialect of his place.
So, overlaps occured in phonemes, and a single vowels was used to express different sounds. This is a natural phenomenon that occurs in natural languages e.g. in English A is used to express the light sound of a as in lap, matt, sat, cat, and that of far, are, car; it can also represent an o like sound in warm, wall, all, Double oo can be used for 'food', 'door' & 'blood' though they sound more like foud, doar, & blud. E can represent e as in hen, or a shwa sound as in amend, u has two sounds 'put', 'but'. The same with o which can represent o as in off, or an e like sound as in worm, work.
This is typical of natural languages, the confusion may arise from dealing with Coptic as a conlang as if it were constructed in one day by one person and that every vowel was put in place perfectly. This in part can be attributed to the dynamics started by Arian Moftah who cahnged pronunciation, and thus had the byproduct of creating the paradigm of thought that Coptic is a conlang where rules of pronunciation can be bent, or developed or changed for clarity or ease, or conformity with other languages.
