Keep the Engineers and Space Jockeys mysterious. They're long gone and all that remains of them are the ruins of their civilisation and their creations. Humanity is very late to spacefaring and all we'll find is scant evidence of what was. Ridley's vision doesn't have to clash with old ideas of what the Space Jockeys are. As sad as it is to see the prequels end, the open nature of Covenant's ending allows for all sorts of material to explore that part of the franchise. I personally consider the RPG to do that very well.
I think the RPG works wonders with the black goo. It doesn't need rules, it's a programmable mutagenic substance which is barely understood. It makes monsters, turns people into monsters, or makes people incubate monsters. It's a goldmine for writers to play around with.
