" They weren't true Xenomorphs, they were protomorphs, works in progress, "
Ridley Scott did a terrible job establishing that in his movie.
It makes sense to me that if David creates those eggs and what we see in Covenant are all protomorphs, just iterations before the xenomorph, that David is going to think at some point 'Hang on, surely I can't build all these eggs myself and keep doing so', and might think to create something that can lay the eggs for him.... hence a queen existing. Which as much as I hate the idea that the Queen then wouldn't be something organic and alien, at least makes some kind of sense.