I think the different "factions" thing is a given, It's like expecting people from earth, from different countries, races, religions, classes, etc to look the same, there's bound to be differences within any society, but that doesn't mean they are necessarily opposite or against each other in the case of the engineers.
I think it's what Janek said, that was a military base of sorts, and space jockeys were either scientists, explorers, travelers or army men, and the ones in the intro were priests doing their ritual, as culturally advanced civilizations do, just different strata of the same society, with that in mind; it reminded me to that quote at the beginning of the 2010 book:
"And because, in all the Galaxy, they had found nothing more precious than Mind, they encouraged its dawning everywhere. They became farmers in the fields of stars; they sowed, and sometimes they reaped. And sometimes, dispassionately, they had to weed."
I think they simply saw how degenerate us humans had become, that humanity spreading across the cosmos was a risk, like a disease, so they were to snuff us, incidentally that was the same conclusion reached by the Alien race mentioned in the quote above, and they had the same intention of destroying us.
As for David, I agree with both of you, I think his main purpose for doing what he did in that concept art was gaining more knowledge via experimentation, but I wouldn't be surprised if there was a hint of sardonic payback in his actions, after all, he's a passive aggressive ****, there's definitely some self-awareness in that android.
Man, everything about the Prometheus-verse is super interesting at concept level, if the movie wasn't so shoddily written I would take Scott's vision any day easily over what the franchise became with Cameron and Aliens.
Prometheus at concept level captures what Alien is supposed to be about; cosmic horror.
Spoiler: 
