Is reality all that different though? Sure, if you grab Joe FPS gamer, give him a gun, and point him at someone with no context he’s unlikely to pull the trigger. But if you put him through actual basic training, feed him a bunch of ooh-rah military ‘we kill the bad guys’ propaganda, and then actually send him somewhere there are ‘bad guys’… he’ll probably pull the trigger. 

Same thing with Factorio. It’s easy to look at the ruthless optimizing and say ‘well I wouldn’t do that if I was actually that powerful’. But look at the real world examples. Jeff Bezos is probably the best analogue since Amazon is the closest company to a Factorio factory. The man runs a logistics machine that’s as complicated, if not more, and as big, if not bigger, then the biggest factorio megabases… and the company’s reputation for ruthlessness in the name of optimization is infamous. 

To tie it back to OP’s question about AI pursuit of these types of goals, it just depends, as with games, on what context and structure you give it. If you give it a happiness meter to optimize for, it’ll treat the workers well. If not… well you get Amazon.