You kind of looped around one of the major plot holes and nearly answered your own question.
Nostromo crewmen find eggs with facehuggers in Space Jockey's "croissant" on LV-426 in 2122, roughly 40 years after Prometheus lands on LV-233. Space Jockey's "croissant" (or Derelict) is there for very, very, very long time. Long enough to be completely fossilised ( and very bloated - about twice the size of typical Engineer from Prometheus story line, if we are to be precise). Therefore the seamonster/Engineer xenomorph cannot really be a seed, "ape" or protoplast to anything in regular Alien xenomorph life cycle, because it is, highly impossible in terms of timeline.
The only chance Ridley had to tie this up, was if he crashed a "croissant" from LV-233 with already fossilised for 2000 years, chestbursted Space Jockey in a chair and classic Alien Queen onboard or classic facehugger eggs premade by classic Alien Queen, straight onto LV-426, where it would stay for 40 years, together with warning beacon until Mother picked up a signal and diverted Nostromo.