It went back to an outpost we can assume exists via inference and context
Or did something else happen to them? Dun, dun, duuuun!!!
but which does not need or want to be explicitly defined, because nobody will do it justice.
True. Brings us to debate of "If they made us, who made them?", which is a bottomless rabbit hole.
I don't really like the word but these Engineers looked a lot like Zen monks, or high space priests, in contrast to the Juggernaut pilots who look more like warriors. But even so, there is a gap of billions of years between the seeders and the destroyers. Still, it's cool to think that what we call Space Jockeys are just one faction of an even larger culture or society. But no one could do justice to that. The mystery makes the concept greater.
In fact, even if the Space Jockeys hadn't been turned into ancient humanity, I still find it fascinating to think of them as the soldiers of an even larger social organism (so to speak), which doesn't need to be explained. Although references do not bother me, as the original Jockey in Alien was once. It wasn't relevant to the story, but its design is so f**king cool, and so perfectly compatible with the atmosphere, that you get excited to speculate about it.