I'm of the opinion that the Space Jockey we see in 'Alien' and the Engineers of 'Prometheus' might not be the same creature.
The Engineers proportions aren't the same as the Space Jockey's, and they're substantially smaller. Likewise, all of the Engineers' tech, vehicles, and buildings are similar to the Space Jockey derelict, but still noticeably different. They're more streamlined and less organic.
The corpse in 'Alien' has visible eye sockets and a tongue, and was (at least in my opinion) pretty clearly some sort of skeleton, not a suit.
Not to mention you can see statues in the Engineers' structure that look like 'Alien' Space Jockeys, with correct proportions and sizes and everything.
My idea is that they're two different creatures, and perhaps the Space Jockeys created the Engineers (Shaw even mentions the idea of the Engineers' "creators" at one point). Perhaps the Jockeys didn't create the Engineers in their own image, but the Engineers idolized them and modeled a lot of their technology on them, and then created humanity in
their image.