NPC would now worship their historical local patron (if he is in the game)
(e.g. Zawty now worships Anubis in game )

NPC factions' god correction applies on new save (while regional discoverable gods apply to all saves).
so if you've already started a campaign and the NPC worship the incorrect god,
that gives you a justified reason to destroy him.

NPC's god is pretty much the same as described in local god crests mod ,
for the gods who don't appear in game, i find the most related god:

Wadjet followers worship Ra, as uraeus always on Ra's sundisk.
Sobek followers worship Set, as Sobek is Set's son, and both are military gods.
Hathor followers worship Isis.
Min followers worship Horus.