Species/WMG

Sil was an attempt to make a Cute Monster Girl of a Xenomorph.
It's just about Canon that the Xenomorphs were created for some reason, so it stands to reason that eventually the Powers that Be (like the Space Jockeys) (or one of their researchers) would try to go in this direction. However, a few problems cropped up:
 * 1) The formula was incomplete, needing a local planetary framework to build on. Therefore, they had to send it someplace with intelligent life so that it would be well-suited for its new home.
 * 2) They set the sex drive wayyyyyyy too high.
 * 3) They overestimated how resilient the local males would be. Modern humans are remarkably squishy compared to nearly every other species.

Sil and Patrick are not the same type of creature.
It would explain certain inconsistencies. Like why Patrick's true form doesn't look anything like that of Sil's son. And why Sil took much longer to develop from fertilized egg to baby than seems normal for her species (she was presumably implanted in a human surrogate mother, and her species doesn't have whatever mechanisms allowed Patrick's offspring to just suck 7-9 pounds of material out of their hosts in minutes, so her early growth was dramatically slowed down). They are related but distinct species (or subspecies - they're obviously interfertile). This theory is also appealing because it removes the third movie's implication that any offspring Sil had would probably have been sickly and sterile so she could never have been a serious threat to humanity. And it would provide a handy excuse for any fanfic writers who might want to throw out some of the things we learned about the creatures in the second and third movie.
 * Since they seem to be artificial constructs to begin with, this makes a fair bit of sense.
 * Remember that Sil's son was still a baby. It may well be that once they enter the pupa stage for turning into adults they may well turn into the more quadruped form as Patrick.

The aliens are a seed/specialized unit of a superorganism.
The aliens are fast-maturing, fast-breeding creatures which seem to operate largely on hard-wired instinct, which isn't a life strategy that one would typically associate with selection for high intelligence. It would make sense, however, if they're specialized autonomous units designed to serve the purposes some larger superorganism, something like the Tyrannids or Zerg.

The aliens were just misunderstood.
They didn't plan Genocide by Supermodel at all. Perhaps they're very keen on genetic modification and given how resilient alien Sil is, they thought they are giving us a gift. For them it was like sending a machete and a hockey mask, because, hey, a machete is a useful tool, and everybody likes hockey, right? Right?
 * Well, according to Fitch they did first give us an infinite-energy methane formula, but when they gave their "friendly instructions" about how to construct a hybrid, they really didn't send their intentions.
 * Going off this, the reason the aliens are so crazy it not because of the alien DNA, but because of the Human DNA. Maybe the combination of both is what drives their aggressiveness and need to mate Up to Eleven and pure aliens are actually a peaceful, benign race. Of course, for this theory to work you have ignore what the scientists said about Mars in the second film, but given that: A) He was crazy and B) The movie was crap, we can just ignore it.

The aliens grow using the same method as plants.
As You Know plants absorb CO2 from the air and release oxygen. They use the retained carbon to grow and thus they acquire most of their mass from the air itself rather than absorbing it through the roots, as one might expect. The aliens may gain mass and regenerate with a similar process, just sucking carbon right out of the air as they grow. This also explains any other conservation of mass problem with aliens in sci-fi.