So I've played all the ones that you've mentioned and loved them (especially Kerbal Space Program), but I'd like to point out that they're fun to play because they're games, whereas similar industrial software applications are not games. This is a very meaningful distinction because the addition of game mechanics makes them fun to play around with.

I also don't think the connections are quite so close as you make them out to be. Factorio is at its heart a survival game -- you can't just dismiss the enemies as added "spice", as they are an integral part of the challenge. The advanced factory automation becomes necessary to build up your tech level high enough to take on the higher level monsters that come at you later in the game.