Not entirely sure about all of that, but that's more due to the various scripts and stories being re-written and changed.
For example, the original working title for Covenant was Paradise Lost, iirc.
it then became: Alien : Paradise iirc, and then Alien : Covenant.
meanwhile, i remember that Alien 5 - obviously AFTER the Alien 1 and 2 events - got 'rewritten' or put on hold due to Ridley's plans with the franchise.
So i wouldn't be surprised if some stuff got mixed in between all of this.
more interestingly though, is that though i don't like the idea that David would be given a too big of a role in the franchise and we'd turn the franchise more away from the xeno into the android, in regarding the obvious fact that David as said by Weyland, 'does not age, and will never die'.
Theoretically, this means that David could actually be used in a story hundreds of years after prometheus' events.
As in, david could potentially be put into a sequal by ridley that is a sequel to the original 2 movies......
again, not the biggest fan of that idea, but it is oddly enough possible, as long as david doesn't get damaged beyond repair.