I feel 'Prometheus' answered this with a question; "They created us.. but who created them? We'll never know. But here's what we do know..."
So my personal head canon like many other here; The Pilots created the engineers, who revered them as gods. Eventually the engineers themselves became technologically advanced (hell, if you want to take into account the hologram on board the derelict in 'Aliens: Colonial Marines', then the derelict was engaged in a space battle with a flying saucer... 2000+ years ago we saw engineers using a flying saucer when seeding Earth (or paradise, depending how you read that scene). Perhaps engineers stole Pilot tech and recreated it themselves - notice the engineers who seeded Earth had no body augments yet. Eventually, like their creators, the engineers created humans in their own image, to be revered as gods... paradise saw a success story, as the human civilisation there flourished under their rule (until David wiped them out) - Earth on the other hand was not so successful, when we crucified an engineer and drove out our creators, causing them to prepare a pathogen to wipe out their rebellious failures. We, like our creators, became technologically advanced and created synthetics in our own image, to obey us..as Peter Weyland put it "we are the gods now" ...and we know later in Alien history, synthetics will design Autons in their own image (such as Call in Alien Resurrection) - the cycle repeats endlessly.
Now the question is; does the cycle of the Xenomorph also loop endlessly... we saw ovomorphs in the hold of the derelict...and urns in the hold of the juggernaut.. in the same way the engineers developed the pathogen based upon the Xenomorph (as per the mural) what would man have created based upon the pathogen? We know what David created (reverse engineered) and he got it pretty darn close to the source, but had it not been a synthetic creating this, I wonder what monstrosity man may have created from the pathogen over time.. perhaps that's what the alien is.. the universe's/evolutions answer and reset button to kickstart the next cycle..the Xenomorph destroyed the pilots, the pathogen destroyed the engineers...perhaps our bio weapon (the Ripley/Xeno hybrid xenos)is what will eventually destroy us and pave the way for Autons time to reign 😂