I don't remember which video it was, but they said that they really wanted players to get to experience the same dungeon from multiple perspectives. Maybe the first time you side with the humans, and you play through one story. On the next playthrough you betray the humans and join the necrotic. Stuff like that.

I suspect that your choices will be permanent for the duration of the run that you're currently doing, but if you restart the dungeon, you get another chance to make all the choices again.