How I reconcile the AI lore
I don't think the Phanes is the ship's AI. I think that the AI is the Second Who Came / One Who Came After (and probably Heimarmene).
The AI fits the best for the one who consulted with Phanes on turning the Third Descender into the Gnoses, considering that it was previously charged with taking care of the Fourth Descender's life support and would probably know how to do it better than anyone.
My overarching concept is that the AI core's ejection is effectively the catalyst for most of HP's actions. Phanes was initially peaceful when he arrived in Teyvat, but after acquiring the AI core (which had knowledge on how to produce mankind), he decided to take control of the planet and create the Human Realm. However, due to his injuries against Nibelung, he became increasingly dependent on the AI to manage the world.
The AI manages the fate/constellation system, and is likely responsible for distributing visions.
You could even argue that the "Heavenly Principles" themselves are really just the rules dictated by Phanes to the AI core that represent his vision for the world.