Terraforming Bay...Ok, wild theory. The Juggernaut in this movie is indeed the same one from the first film. The engineer's ability to Terraform was mentioned in a script for Prometheus. That's how shaw hooked weyland on the expedition. That incidents throughout history (the great flood) were the result of Engineer Terraforming. So Daniels (maybe knowing little about the alien's ability to withstand harsh environments) uses the technology to destroy the planet (or at least make it as unstable/hostile as possible) in an attempt to destroy all traces of david and his creations, and prevent any future human interest. Paradise then becomes Hell.
In the pray trailer, it appears the covenant is heading down towards the planet surface. That coupled with the earlier pics of daniels and a male companion seen on the surface standing back to back holding weapons, has me thinking they've escaped back up to the covenant, survived the on-board mayhem, then set down near the end of the movie, with Daniels planning to use either engineer technology, or overload some kind of terraforming tech on the covenant to destroy everything. As for the body in the original derelict, Maybe David planned to blast earth, but shaw's hologram show's how to over-ride the system to fire right there on paradise, but she disappeared or was killed mid-attempt. An infected Daniels enters the seat an initiates the sequence, before succumbing to the final and perfect form of David's Alien, i.e. the Chestburster.
The derelict then sits on the wind swept hill, paradise destroyed, the hole in the floor, the Alien queen laying her eggs. Waiting for something to come along. Who knows, maybe David survived long enough to activate the beacon. Maybe he found a way to get his creation to earth anyway.