My understanding is that we're still not 100% sure what was found on the original ship on LV-426 in Alien.
The Engineers created the base bio-tech that can lead to xenomorph-type creatures. We saw one form of this in Prometheus, and another form in Covenant. But neither are exactly like what we saw in Alien 1-3. With the cliffhanger that Covenant ended with, it could be that David goes on to make the eggs that we saw in Alien. But it could also be that the original ship was just a different crashed Engineer ship carrying slightly different eggs. Future movies may tell, or may not.
The crashed engineer ship in
Alien feels too old. I mean, the engineer guy has been lying there dead for so long, he's fossilized and has fused with the ship's controls. My guess is he got infected by the black goo stuff at the base in
Prometheus and fled on his ship. His ship probably crashed on LV-426 when the xeno burst from his chest. It then proceeded to lay eggs in the hold ~ or maybe those eggs were already there, and one hatched and got the engineer after the ship had taken off.
Either way, I think it's more likely that David simply tipped off Weyland-Yutani about the existence of the xenos and the engineers and such after he fled the engineers' homeworld, and then the company went looking for the engineer ships (hoping to find some xenos inside) and found the one on LV-426.
I do hope we get some sort of resolution to the
Prometheus /
Covenant storyline, but I'm not holding my breath on that one.
EDIT: It seems like
some people are saying that the space jockey isn't an engineer because of the size difference and the fact that it looks like the space jockey isn't wearing a suit. I'm seeing some arguments online that the space jockeys made the engineers, who made themselves tech that resembles their creators. Inside the engineer spaceship seen in
Prometheus and
Covenant (and the short film set in between), you can see glimpses of giant "statues" that look more like the space jockey than the engineers.
One interesting thing to note is that the original "space jockey" from Alien is much larger that the Engineers we saw in Prometheus. It's been left unclear if this is just a minor continuity issue, or something of meaning.
I thought that
Prometheus resolved that by showing that the engineers wore big, bulky space suits with "elephant head" helmets.