Coptic is the only stage of the Egyptian language whose vowels are written, which makes it the foundation for everything said about how earlier Egyptian was pronounced. That does not make its own pronunciation transparent. The written record shows which letters a word took; it does not show what those letters sounded like in a mouth.
For the Greek derived letters there is good comparative evidence, because Greek pronunciation of the Roman and Byzantine periods is itself well studied and Coptic borrowed a system already in motion. For the seven Egyptian letters the evidence is thinner, and janja and kyima are the hardest of the set, because they write sounds with no Greek counterpart and their distribution differs across the dialects.
Scholars work from several kinds of evidence at once: the way Coptic words were transcribed into Greek and later into Arabic, the spellings Coptic scribes used when they had a choice, the correspondences between dialects, and comparison with the wider Afroasiatic family to which Egyptian belongs. The result is a description with confident parts and uncertain ones, and honest grammars mark the difference. The living Bohairic of the Coptic Orthodox Church sits alongside all of that as a separate kind of evidence, continuous and real, but not a recording of the fourth century.