The entire point of Covenant story is to show exactly how the alien was created. Like it or loathe it, that's what they have done and that is the intention. So yes, as it stands right now David is the creator of the Alien and everything that came before from the EU is no longer relevant.
People can oppose this by pointing to the murals in Prometheus but Scott has admitted the story has changed since that time. When Prometheus was released I believe the intent was still there that the derelict had been on LV-426 for thousands of years. But that has since been retconned. The facehuggers on the mural and the painting of the xeno holding the egg are not even visible in the film if I am remebering correctly so it is a mute point anyway.
However, what Prometheus still shows is that some form of chest-bursting existed prior to David's experiments as did The Deacon. As it stands David has definitely tinkered with pre-existing things but the xeno as we know it is definitely his creation.
That's how it is until a following film decides to change it again. Suggesting David is simply replicating an eons-old Engineer recipe for the creature is just fanon in the same way people force Peter Weyland and Charles Bishop Weyland into the same timeline.
The point of the film is to explain who/what created the creature. They have now answered that. If it is just replication it renders the entire film and its story pointless.