What Prometheus is 90% nonsense and Covenant is pretty much at that level whenever it starts talking about the origins of mankind. I am also of the opinion that both movies have so far impoverished the series with their need to provide a backstory for the xenomorphs and to put other things in context. That said, they do add interesting information when you look at the series from a wide angle, and that's what I wanted to talk about.
In the original Alien, the xenomorph is a perfect human killing machine. Because we know nothing of its origins, the natural assumption is that the creatures evolved naturally somewhere. The one thing I give the prequels credit for is that they provide a reason for the xenomorphs to look so much like Terran animals and to be so perfectly suited to the human anatomy where reproduction is concerned.
They also explain why that species is so flawless: it was genetically engineered by a demiurge seeking perfection. David is himself an imperfect creation of a species he perceives as failed and considers himself above later models who lack some of his more particular idiosyncrasies.
The proto-xenomorphs, like the humans, were the product of the Engineers, a species supposedly superior to humans, whom, like David, they sentenced to genocide, as would gods.
The story of the prequels is one of a succession of species giving birth to each other, each successive one destined to surpass or disappoint its predecessors. Sometimes Yahwe drowns his creation, other times Zeus murders his Chronos. David and the xenomorphs are the only pairing who do not have an antagonistic relationship. The Gigerian slayers do their creator's bidding by slaughtering the humans from whence they originate.
Just wanted to throw it out there. I am not sure what conclusions to derive from it all.