...now, do players go wildly beyond achieving that victory condition in ways that play into the colonial-exploitation vibe? Perhaps.
I always kind of embraced the idea of being the bad guy in this game. I find the ease with which I (and others) just kind of shrug it off intersting.
A more stark example would be the movie Starship Troopers: superficially, you might feel like the "bugs" are the bad guys, but take a step back and you realize that the humans are the ones attacking them.
As for accepting it, I'd imagine it's because the game doesn't really give you a choice. There isn't a way to coexist with the native species -- they're always aggressive even if you don't create pollution (they're just not drawn to you without pollution; they'll always attack if they see you). In your metaphor, it'd be like if we never did anything but shoot at the alien. So you can either just not play the game at all, or you can exist in conflict with the native species.
It'd make it a very different game, but it'd be interesting to imagine there being some way to work with the native species. If you could make the choice between a quick and dirty pollution-heavy resource-extraction "bad path" and a more complex social cooperation "good path", that'd probably trigger you feeling guiltier about casual extermination.
In Starship Troopers (this varies between the book and the movie), as I recall, the bugs are more or less a peer species to humanity. They're engaged in territorial struggle, which escalates to war. (The movie version engenders a lot of debate over whether the inciting incident of the war was a false flag by the earth government.)
Also, is this planet like ten square miles large or something? How much damage is the character doing to the planet as a whole? We all willingly pollute our own planet in a much more severe way to do nothing more than make our own lives a little more comfortable, and I don't think that makes us evil, either. Short-sighted, maybe.
The character is not supposed to die, they're supposed to be evil. The point of the game is that winning the game is evil. It's not saying humans on earth are evil, it's suggesting that maybe they are, or maybe we're the bugs, or maybe some of us are the bugs and some of us are the engineer. We also don't know the intelligence level of the bugs. They're smart enough to coordinate attacks, pathfind, target polluting and military buildings, and sense pollution, but it's purposely ambiguous.
That same mod also uses a tech tree mod that actually makes the burner phase slower, so you pollute more in the beginning to boot.
I love the game and I usually like to play by minimizing my pollution cloud (rushing solar and nuclear) and trying to avoid the natives as much as possible trying to be "good" but still survive, but in the end you still must make a factory and eventually piss off and kill natives, ultimately its you or them, I know I am the monster not them.
But as creatures in Factorio don't have triggers that force us to feel empathy for them, what objective reasons do we have to take their side over a protagonist, who is clearly human? The only reasons I can think of are violations of private property — which the monsters don't see to actually claim — and non-aggression principle, which they usually break first, giving the protagonist the right to defend himself.
> Pollution attracts biters to the Player's factory. Biters who find themselves in a polluted area will attempt to reach the source of pollution and destroy it.
So you can say they are the ones in self-defense.
There's also the expansion groups, which will periodically move around to create new nests. Even if you don't walk at all, you will be found and attacked sooner or later.
That said, the actual goal of the game is to build a tech tree, launch a rocket, and escape the planet.
(But once you get things going, most folks just keep building and launching rockets, elon musk style™)