i don't remember where, but i recall something of a raven or crow working for athena and it's implied they manipulated past masters behaviors somehow. the trio of vultures you described seems to relate to the trio of observers revealed on rutheless route, unless it's just a coincidence. considering that we learned on how some of the gods left something of their influence over the labyrinth, there's a good chance they are some form of divine intervention. i'll admit for the sake of puns that the presence of these vultures "flew over my head" as i do not recall reading those lines.
Oh yeah, if you or anyone else finds quotes in the game about ravens/crows/any birds working for Athena to influence the past Masters, drop 'em here for sure!
You posit an interesting link with the vultures we see with Nikos and the 'trio of observers', especially since I did mention that the Narrator did just directly talk to the player before the vultures are seen... I feel like we would be seeing more of said vultures in the Ruthless route, though, and the only time I can think of might be when something lands on the roof of the Hotel right in the beginning of chapter 1 when Luke and Kota are plotting to ditch the Hotel? I suppose there is also space for the observer that appears to Nikos in Ruthless chapter 2 being in the form of one of these vultures, and Nikos would not describe them as such, knowing they are instead a god come to answer his pleas... so maybe this holds more water than meets the eye.
And no worries, it didn't take until my second playthrough that I stopped and said "Wait, vultures? How is there wildlife?", haha.