I think its great fun trying to make them fit. As I say, I saw (I think on Alien Theory but I could be wrong) a piece that made AvP Bish fit with Prometheus Weyland.
The debate is fun... and I'm glad that Michael Bishop's funny ear has been explained - I never realised he was enhanced... and never really got the whole funny ear thing.
OR he's a replicant and we can have the "is Blade Runner part of Alien-verse." (In my head, it is. As is Outland.).
Canon seems to be a transient thing for Fox - as someone pointed out, ACM was the official sequel for a bit... that was the final word. Until it wasn't.
As for the other part of this conversation; it seems to me no one apart from Ridley seems to think that David creating the Alien is a great idea... but that's what we've ended up with. I DON'T think its open to interpretation - even if its a shit idea, its the shit idea that's the "reality."
Then again, he also states in his commentary that the xenos can now put themselves back together like a T-1000 - thank goodness THAT didn't make into the film.
As has been said - hopefully the mess that Covenant left will be cleaned up in a final movie.
Also, as much as I want AvP to fit into Alien as a whole, we can twist and turn and make it work by and large, but it really isn't.
On the other hand, I wonder if it works better that the AVP is part of the Predator-verse and ignores the events of Prometheus, A:C, Alien and so on (until we get that Predator movie set in the future vs Colonial Marines).