Covenant doesn't have to confirm that. AvP movies are cross-overs. They never been part of canon.
According to who? Both the AvP films and Prometheus/Covenant are produced by 20th Century Fox - and they have never (as far as I am aware) confirmed what is canon or not. The default position until Covenant was that they were canon due to be produced by the same company. Covenant confirms they are not though.
Let's not forget Alien Colonial Marines were cannon for a certain time.
Fox didn't make a official canon, AvP is not officially a crossover.
Alien, AvP and Predator media cannot make a coherent cannon without butchering the whole thing with time travel and extremely improbable scenarios.
It is possible to create multiple possible cannons however in every one of those some content has to be rejected.
Do we really have to push our favorite version of cannon down each others throat to feel better about the whole thing?
Simply make your own version of cannon that suits.
My version of cannon has Prometheus, A.C. Alien, Alien Isolation, Aliens and Alien 3 (+ some other content) as Alien cannon. It is elegant, it has no holes, and I had also ejected Alien Resurrection from it and placed it into "that shitty alien movie" universe.
And at the same time I had made my own AvP cannon that includes all Predator movies, all AvP movies (and 2 games) and some Alien movies.