I would like add another factor: the alien or Engineer timeline. We actually know nothing about it. All we have seen is a corporate timeline. It’s in the rule book, and you can figure it out from various books and other sources. But there has to be another, probably much older alien time line, with many other events, mostly unknown to mankind.
My intention is NOT to write such a time line, at least not a definite one. I think it would just kill the mystery that is the centre of this franchise. But just knowing that such a timeline must exist makes it possible answer the initial question in this thread in another way: WY, or at least some factions within the company, does for sure know about the eggs, the xenos, the engineers and the derelict. But I would say that it’s at least possible that someone is having an idea of even bigger things. Not an entire mythos chronology, but fragments of it. Perhaps an ancient war, events of interstellar migration, the building of certain facilities etc. At least there must be some theories about it. Being able to grasp parts of a huge unknown is also a kind of knowledge.
I imagine that WY probably has some kind of secret archive (an actual location, imagine a visit there) with bizarre artifacts. It would also seem resonable that an advanced corporate AI has done some calculations, trying to figure out some kind of alien chronology. So rather than actual knowledge, it could be a speculative hypothesis, or several. I imagine a possible mythos timeline with huge gaps.
In a way, this is a way to emphasize the Lovecraftian perspective: mankind is a insignificant part of something much bigger. There were others long before us, and they also have a history. But we will only be able to grasp it with our very limited human ways of understanding things.