That is of course not to say that the developer is worse for it, far from it: a developer that can create a complex game based on simple rules is a better developer imo. But that doesn't mean the rules (and therefore programming them) aren't simple.
Still, the scale of the mechanics leads to more complexity than your average crafting game. If your interpretation of what linkdd wrote is correct, his point is directly controverted when considering that threading discussion in the article. If you know the history of Factorio, then you also know there are many underlying, interlinked systems like that in the simulation that are complex. The software must handle all the ways in which those subsystems could possible interact.
The comparison to Dwarf Fortress is apt. Another similarly complex game that comes to mind is Distant Worlds: Universe, a 4X game that, with all the managers turned on, plays itself.
As to your assertion about the game play of Factorio, it is not mine, craft, and place like in a normal RTS. In order to succeed at the game you must design which is a far cry from base building in StarCraft II, for example. Blueprints are indicative of this design requirement.
There are games where you design ships and save templates for them. But playing Factorio all the way through is a much more complicated experience than movement and crafting. Unless your assertion is that complexity of gameplay is measured by input mechanics, which I think is demonstrably incorrect.