The gameplay is building a factory. An example of a more sophisticated interaction with the in-game "nature" is Minecraft: there the living things just become a part of your factory.
The simulation in Factorio isn't "harmful", it's just incomplete (in a way the author of the post doesn't like) because the implementation has started from the factory, not from the world (like Minecraft or Dwarf Fortress did).
> the implementation has started from the factory, not from the world
This sounds plausible, but I'm not sure if it's entirely true: the factory building is explicitly set in a foreign world and not in our on as any of the many many other factory sims out there.
I think it is more like the authors had the "fight against xenos with factory" idea as a start and then got severely detoured into the factory building after they had the basics of the world done.
I didn't have a feeling that it's set in a foreign world. It looks like some ugly moving things got slapped on the map because in a video game you naturally have to shoot things.
When developers want to pass a message they use catmen from the Avatar movie. Imagine changing alien models to that. There will be another whole layer of questions.
The simulation in Factorio isn't "harmful", it's just incomplete (in a way the author of the post doesn't like) because the implementation has started from the factory, not from the world (like Minecraft or Dwarf Fortress did).