I think that's the direction the prequels are heading in.
Up until now, there was still at laest some
kind of hope that might have just been a red herring. I guess that, if that's what the quote is
alluding to, that's how it is now.
Except that having been engineered gives them purpose; and for story telling a purpose is essential. The genetically engineered dinosaurs in 'Jurassic Park' had purpose even if they were just considered to be theme park attractions. It's when that purpose goes awry the story becomes worth telling.
I'm sure that's where Scott is taking this whole trilogy.
No, it either gives them an old, now-irrelevant purpose or, alternatively, just makes them a mere biological experiment.
In both of those cases, it makes the creatures a lot less
potentially interesting. If they arose naturally, it implies there's possibly still an ecosystem out there so
dangerous, that the Alien's "structural perfection" came out of biological necessity.
I always loved that quote from one of the novels, where a character theorises that, on their own planet, they might be little more than the mice. Thinking of that really
fired my imagination, making me picture a truly nightmarish ecosystem of all manner of cosmic horrors. It would bring the Alien as close as possible to O'Bannon's original concept of them being somehow related to Lovecraft's blood-thirsty deities: An unholy natural selection, as it were. It makes the Alien a fragment of something potentially greater
and even more murderously obscene. An entire fossil record composed of deathly terrors.
If they turn out to be just an isolated result of bald dudes f**king around with a petri dish, to me, that devalues the Alien as much as the Engineers devlued the potential of the Space Jockey.
To me, that's an infinitely more thought-provoking question. Not, "Who made them?" But, "What kind of environment could be so
horrifying that evolution selected
them to survive?"
Aliens don't need to have been artificially created for the purpose of a story. Story = goal(s) + obstacle. Aliens always take up the 'obstacle' role, regardless of their origins.