You are not supposed to get the tadpole dreams if you aren't using their power. You also won't learn about Raphael unless you talk to Nettie and the game narrative support never meeting him. The game is full of elements like that.
As for the companions, their triggers/checks are all over the place and buggy right now.
I came across this Nettie bit before and even than I was pretty sure it's wrong. Anyway I tested it and Raphael doesn't necessarily comes after meeting Nettie. He come after the first time you find a lead that is a goose chase. Specifically, I was able to make him show up after finding the githyanki, after visiting aunty Athel, and after speaking with gut. In all of this cases I had no interaction with Nettie whatsoever
