Everything on board the Derelict is leftover from David's experiments on the crew of the Covenant. The eggs, if we're to believe that Shaw's ova were the excavated, experimented on via the black goo, and either themselves or the products that would lead to the prototype Alien eggs. Then those eggs seen in Alien had to come from somewhere.....leading me to believe that they were victims of vivisection by David similar to Shaw. The Pilot could have been anyone either....
It doesn't even have to be a Covenant crew, it could be anyone. Maybe David lost and just sent a back up Derelict filled to the brim with his "progeny" somewhere, and it happened to crash land on LV-426. Now this begins to fall apart with, "Where did David get the Derelict?" Let's just assume that he has knowledge of where Engineer outposts are located at this point and is headed towards one, or by any other means he acquires them on a crusade to wipe them all out. That's dumb.
The second part is comically villainous. The first part, is pretty f**ked up though. Maybe enough for the idea of Alien Covenant to take on an even more horrifying context, like the work of a serial killer with the kind of methodology to make something like this work...tell me your thoughts on the idea. It would be a pretty brutal twist that negates the sudden corny implication of Covenant that David made them all, at least to me. If this is the scenario they're going for David really is an Android ShirÅ Ishii, or Ed Gein, Jeffery Dahmer....which is again, corny. I don't know if I like the idea, but I think it's where they're headed with this.
But it does add a completely new level of horror to the Company's interest in sending the Nostromo crew to investigate the Derelict, and the discovery of the Derelict at all. They're not exploring an Engineer ship as much as visiting the abattoir of the results of human chemical experimentation, vivisection, who knows, maybe even rape.
That's dark. A bit too on the nose, and how David does all this, I can't say it wouldn't be corny. But the idea by itself that the Derelict is more of people uncovering the abattoir of a serial killer, and possibly serial rapist on a nightmarish scale. That, just makes sense to me as the direction Ridley wants to go with this.