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.
I get that they are games at the end of the day, but many of the elements/mechanics seem to be from 'real' software (in this category of game). It's not a criticism, it's just an observation.
For more on how to go into video game theory, PennyArcade's XtraCredits series is pretty binge-able: https://www.youtube.com/channel/UCCODtTcd5M1JavPCOr_Uydg
http://store.steampowered.com/app/271240/Offworld_Trading_Co... ?
I haven't played a game in the longest, mostly because I find it hard to justify the time ... I've been reading lots about economics and finance and if I can get some "experience" to solidify the concepts while still having fun at the same time then what the hell, I wanna do it!!
(No I'm not making the spreadsheets in space joke.)
Edit: Pipe Dreams(?) about 20 years ago, and more recently Where’s my water.
To me, Factorio is very basically just simplified Eagle with monsters (Eagle is PCB designer software). You have underground belts (vias), smelters (ICs), inserters (Caps, resistors, 2 lead parts). Then you throw some monsters in there to give some random fuzz on the designs and make things a bit more 'spicy'.
Mincraft is much the same, it's a very basic Solidworks. You can extrude and loft with the voxels, put in some basic digital electronics (redstone), some basic fluids (water/lava), and make simple machines (look at mob-grinders). Throw in some randomness with the creepers and other mobs to make things spicy.
Kerbal is also the same. It's a basic flight simulator. You can mess with staging, centers of mass, and centers of thrust. You can do simple ballistic and orbital mechanics. Then you throw in the wonkiness of the physics simulator and the fan-named 'Kraken' and you have the randomness of monsters (I think they could have done better in this regard)
A lot of these 'indie' sleeper hits seems to be like that: Take some industrial design software, make it so basic a 7 year old can use it, throw in monsters to mess up the designs and to shoot/stab.
Other software that could be used for this process is Z-max (optics design software), some kinda Wall-Street software that's not just excel, maybe some urban planning but better/more random than SimCity/CitiesSkylines, other stuff.
Any ideas?
EDIT: Here is a wiki page of possible avenues: https://en.wikipedia.org/wiki/Category:Computer-aided_engine...