Ok, which leads up to something I wanted to talk about [don't read below unless u want spoilers]
Ok with what happens at the end, wtf was with the discovered dead pilot in Alien? I would remind you then that there were multiple stasis pods housing other engineers; the dead pilot was probably someone who woke up much later at a very bad time and attempted to get the ship flying again.
As for the xenomorph going from what was birthed in the aftermath....we saw how the black ooze, this bio weapon that seems to break down dna and rearrange it into new life had produced several different varieties of creatures, from "super worm of death", micro organisms that zombify its host, giant tentacle "hugger", etc. What likely occured between then and Alien was mass hyper-evolutionary warfare; all these different lifeforms and multiple generations after them clashed with eachother until the xenomorph emerged the sole survivor, layed eggs which would lay dormant until other life disturbed them.