Its possible that Xenomorphs could be both natural and artificial, for example they could have started out as a natural but aggressive species before being introduced to the black liquid, its one theory anyway and I seen some say the same more or less.
As for Mass Effect 3, no problem with the endings here either, I agree that melding flesh with tech could be seen as a form of indoctrination since no one gets a choice and a new mindset could possibly develop. However, I would not mind the Leviathians winning, especially when compared to the Reapers since they give their subjects free will and peace so long as they get tributes now and again.