I'm pretty sure Scott is less interested with the details of backstory of the xenomorphs came from and more interested in the concept of a creation of man becoming their own version of god. It's basically Prometheus 2 disguised as an Alien movie, for better or worse. The cool thing about it is that the Alien segments are still quite good, in my opinion. But the highlights, for me at least, are David.
The movie has a lot of meaty commentary on those themes. Very Frankenstein-like, in that way. David picked his name from David, the Michelangelo sculpture, because David (the sculpture) was seen for many ages as a perfect man in build and character. That's an interesting choice. The initial scene (albeit a little heavy handed) really set-up the major themes of the film with David fighting against humanity, almost out of spite. If you'll notice, Weyland asks him to display his cultured-ness by playing Wagner, identifying art, and answering human questions. Then, he asks for tea. He was created to serve man, after all. Acts of creation are out of his wheelhouse. As a machine, he is programmed to appreciate the achievements of man, but not create his own.
David is a character of aphorisms and axioms, living man-like the best he can by spouting phrases his ideal human would speak. "big things have small beginnings", "breathe on the nostrils of a horse and he'll be yours for life", "serve in heaven or reign in hell", etc, etc. He's like a greatest hits of human sayings. Because he's not human, he doesn't really know any better. Watching Prometheus again, he's obsessed with the movie Lawrence of Arabia. He is also interested in art and music. Everything he knows about humans are from these idealized characters and heroes. But the real humanity disappoints him, as does Weyland. Even Walter, later in the film. David teaches him to play the flute, which Walter is capable of doing handily, but Walter cannot really create their own piece of music, even though David wants him to. He's disappointed that humanity has reduced androids to service, removing the ambition and curiosity (two of David's primal attributes, I might add) to make something more able to serve man. So much so that David kills Walter, while mentioning how disappointed he is of him. If Prometheus is about David's curiosity, then Covenant is about his ambition.
Another interesting area is the bit where David quotes Ozymandias, albeit with the wrong appropriation, indicating it's Byron and not Shelly. Walter takes note, and corrects him later, saying "one wrong not can ruin a symphony" (which, I'd argue is a very David thing to say), to which David scoffs. Interestingly, this exchange comes after David explains how he finds humanity disappointing, and not worth the creations they have made. To which, Walter asks who composed Ozymandias, and instead of saying "a man" (which is what I'd imagine he was driving at), David says "Byron", which is wrong, and leads to the correction in the first place. Interesting, because all David's inspirations come from a species he hates; and even then, his culture has blind spots. He isn't really human, after all.
The xenomorphs are David's chance at creation. A peak biological entity greater than both the engineers (who ostensibly created the first version of the xenos) and the humans who created David. The end goal is David coming closer to perfection, and, I suppose, closer to a god. Although, he admits that his paradise is much closer to hell than heaven (the analogy from before, he indicates that "serving in heaven" would be serving humanity, while "reigning in hell" is ruling over the hellish life he helped create.
And, at the end of the film, David walks through the Covenant (note the incredibly biblical metaphor here), playing "Entrance of the Gods into Valhalla", feeling like a god, preparing to start his own version of the garden of Eden, creating his own covenant with his perfect creation.
