The application is that I'm trying to ascertain sound changes in the
Nilotic Luo languages
I can tell you that when I read professional linguistic literature, I usually face with ad-hoc transcription systems, without any proper description. The professional comparative linguists even when dealing with Russian that contrasts the two, often use "j" where there is no such sound! For instance, I often see things like "bjelo" when dealing with Russian, even though this field requires precision in depiction of phonemes!
Below is an excerpt from Fortson's "Indo-European language and culture". All listed words are supposed to be Russian and used to analyze sound changes:
But what??? How does he indicate palatalization? In multiple different ways!
At the end of the words he uses apostrophe, except the word kakoj where he does not indicate it at all. In the middle of the words he either uses "j" in words that do not have this sound (knjaz', desjat') or simply does not indicate palatalization at all (čtenie has all 3 consonants palatalized, but it is not indicated by Fortson, dennica has 2 palatalized consonants, d and n). In word desjat' all 3 consonants are palatalized, but Fortson does not indicate palatalization at all in the first case, uses "j" in the second case and apostrophe in the third case. Three different methods in one word!
How one can arrive at precise reconstruction of an ancient language if he does not distinguish different consonants in a living, widespread language, where these differences are phonemic and etymologically determined?!