On the appearance of the Alien in A:I, just wanted to point out that with the inclusion of Prometheus, all bets are out the window, since the origin can come from ANYWHERE, not just the usual planet, or something that's been hiking through space.
If you look at the continuity, Prometheus occurs before Alien, so the two would be historical, while Aliens, Alien3 and Alien:R would be unconnected at this point. On the assumption that they designed based on what the inworld characters would know, no one would be aware of what a Queen is, or what the actual lifecycle of the Alien would be, and I hope the game lets us find out.
For the topic of the lifecycle and contrast between the Queen and cocoon forms, I don't mean to throw fuel into the fire but if you recall, AVP2 introduced a third form of replication by the Predalien by physically using the inner mouth to implant embryos into the victims. Multiples of. So lifecycle can be as much a creation of the director as anything else, and what future directors down the line take for canon is up to them. The canon is flexible and evolving in that way.
However, I must point out that some comics and novels have clearly stated that the two forms of reproduction can take place, depending on the presence of a queen embryo, or if it has to grow into one. The Alien was stated to be able to evolve, after the Aliens films.
So Alien->Cocoon to get more Aliens->morph into Queen->Eggs
or
Queen egg->Queen embryo->Queen