This seems to me like something that may ending being a mystery or something of an "oops" thing. I am not entirely sure which way it goes for now.
In Alien: Covenant, In one of David's flashback to when he arrived to the white people planet. He was docking with a huge floating curved stapler (not sure how better to describe the shape) structure before that horrible thing happened.
Earlier before the above event, David flew/crash, not sure which since he clearly lied about that bit, into the forest close by to the Necropolis. The floating stapler dock structure is nowhere to be found. Could they have escaped their own weapon in the stapler structure? I am asking this because in Prometheus their starship are capable of atmosphere manipulation and perhaps could have escape that horrible event. Or were they caught and if that is true where did they fell/crash? There are a few aerial flyby especially with the crane scene. All we see of the Necropolis is stone after stone. Not even a single crater to explain the disappear of a HUGE freaking structure?!
I sincerely hope that this was an intent teaser meant to lead to the next Movie rather than a production mistake!