1. The aliens, and the alien queen, in Aliens are intended as natural animals, as is the creature in Alien 3.
The creature in Alien was broadly assumed to be natural, until Ridley retconned everything with Prometheus and confirmed them to be a bio-weapon (he dismisses all Alien films not made by himself).
So it all depends on whether you consider the prequels - Prometheus and Covenant - to be canon. While I like those films, I personally only consider Alien and Aliens to be canon.
2. Yes, according to Ridley. It’s not 100% clear how because Fox foolishly scrapped his third prequel (and made the weak Romulus instead 🤦🏻♂️) which would have made the connection. However, it’s clear that David used a huge batch of human embryos combined with his two facehugger embryos to create scores of alien eggs.
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