Filling the blanks: tying PROMETHEUS to ALIEN
I think most of these assumptions are correct. I stand by my feeling that the mural of the xenomorphs on the wall and ceiling implies a religious connection. The one on the ceiling specifically is a Geiger painting of the xenomorph lifecycle which, when put on a ceiling, creates an undeniable Sistine Chapel connection. I think the Engineers worshipped the xenomorphs and were trying to create creatures in their image.