I don't know if they'd all get eggmorphed, but yes, my suspicion/fear is that the survivors of Covenant would head to LV-426 and suffer an unfortunate fate - leading to David's new creations being placed on the derelict juggernaut.
Rather demystifies Alien altogether, as opposed to Prometheus and its story which, while imperfect, at least preserved the larger vague mystery of the epic cataclysm that destroyed the Engineers and led to their dead being strewn across the galaxy on various planets like 223 or 426. We don't have to know everything to know that terrible things happened with their experiments thousands of years ago and something they created destroyed them, leaving their vicious weapons behind - which is what we essentially had been told for decades about the derelict from Alien. As opposed to, let's say, a renegade android planting the eggs there 20 years prior after cooking up some aliens and a fun summer bughunt.