I'd give PAS Spinelli a pass here and say that the revelation that David created the Alien is a retcon, since in the original film the Derelict and its cargo of eggs were intended to have been ancient at the time. Covenant's new revelation on the origin of the Alien that shifts their creation to a more recent event that David is now responsible for is a retcon that I find to be fascinating both in Covenant itself and in the way its implications ripple through the other films.
As for "film canon being messy and nonsensical," I don't really mind when things don't gel 100% in a franchise I follow. Creators' ideas change (and in the case of this franchise, we've now seen multiple creators with their own ideas come and go); the Alien movies have never been a true ongoing narrative. Each movie is, essentially, a standalone outing that says what it wants to say and moves on. Alien 3 had to concoct a nonsensical way to continue on after Aliens. Alien: Resurrection had to do the same to Alien 3. Prometheus and Alien: Covenant shifted the trajectory of the story to a more mythological exploration of creators and their creations (and even in the isolated case of these two movies, Ridley changed his mind about certain ideas from Prometheus when he started working on Covenant). Hawley's show will likely find its own path and alter core ideas we hold about the franchise again. An ongoing series like this with multiple creators that shifts focus or prerogative or muddies the "canon" in attempt to do something interesting doesn't bother me in the slightest; I'd rather see them keep taking big swings, even if there are some that don't quite land. I'm much more interested in stories (even stories within franchise filmmaking) as individual artistic interpretations than I am in them as points on some arbitrary, fictional timeline.
