In my head I kind of rationalize it that the Engineers in Covenant have been all but forgotten by the more "perfect" members of their race, as the more "godlike" Engineers (like those seen in Prometheus) left the homeworld long ago and the stragglers on Planet 4 have since been withering away, losing their hold in the galaxy, and dying off - with David then putting the final nail in their coffin as he eradicates them. That parallels nicely with what David's thoughts on humanity, too: "They are a dying species, grasping for resurrection. So they are leaving the earth forever. But their power is an illusion. They don’t deserve to start again, and I’m not going to let them."
I do believe that there are more Engineers out there, though. Like what we saw in Prometheus, or the Space Jockey in Alien - beings that are further evolved, to varying degrees, beyond the humanoid forms in Covenant (almost certainly due to varying degrees of experimentation on themselves with the pathogen).