In regards to the ending(s). It was luck the engineer pilot found Dr. Shaw in the escape ship, and luck her that the monster killed him. Because if the pilot had survived the tentacle beast, he'd have just hopped into another ship and attacked Earth.
Also, since when do aliens emerge from dead hosts? (The pilot Sure looked dead.) Sure, it not quite the xenomorph we are used, too, but it's also something else we can (have to) explain with the biotech goop.