Fair points, Beagle.
The "squirts in space" comment made me laugh because it's so true, we're not just squirts in space, but squirts in time as well.
Our very existence right now is basically one nano-second to the universe as far as time and its age are concerned.
And when I say "god", I don't mean something fantastical. I mean something so advanced and incomprehensible that our minds can't properly understand it. (There's this theme I liked in the Elder Scrolls, I know it's a fantasy setting, but the "Planets" up in the sky of that setting are actually the physical gods who are infinite - but because mortal minds can't comprehend infinity, you instead see a round planetary object instead.)
What if something like this is the case in Alien, a being comes from a different dimension, due to its utterly alien nature hailing from somewhere with laws of physics entirely different from ours, our minds may struggle to grasp them - and they may struggle to grasp us too for all we know.
And sufficiently advanced technology can seem almost magical in nature. The corrupting force of the Black Goo stretches the boundaries of science as we know it, but to the Engineers it might as well be something some kid cooked up in his nan's basement for fun.
That's what I love about Alien, that we're literally amoebas who have discovered a world beyond ours and have ventured into it only to find beings ahead of us. Imagine ants discover radio technology and realize that some giant hairy bipeds have been using this technology for a very, very long time (especially in ant lifetimes). That's humanity when compared to Engineers, Space Jockeys and hell, even Predators who see us as nothing but dumb animals to be hunted for sport.
We're truly bottom feeders, searching planets for resources like sea cucumbers search the seabed for food. Our ships are literally space cucumbers man! We're so puny that we're probably unnoticeable. imagine how daunting that'd actually be? To find out other intelligent races knew of us but ignored all our signals reaching out for the stars? Or the reason Engineers didn't destroy us was because they realized we're not worth the resource wasting trip to Earth? Maybe the one awoken by Weyland was either a fanatic devoted to that cause or someone ignorant of the change? Maybe they saw us as such lower lifeforms that when we breached the barrier of the Sol system, they were all like "wtf? So they actually did it?"