There are a lot of things that mods can't do (these would be mainly the candidates). Or things that mods can do, but not in as optimised way as we can do.
Also, we would always make things little bit differently even if something similar is done by mod already.
As an example, I give you the blueprints.
There was actually a blueprint mod before blueprints became a thing in the base game:
You had a special item that you could build to specify 2 corners of the blueprint to be stored. Then, through some gui, you selected the blueprint to be built and then you had to build different entity that specified the position of the blueprint to be built. It spammed that blueprint on the map instantly for you. It was interesting, but very clunky. Compare it with what we have now, blueprints as items with tooltips that contain preview of the blueprint. Instead of just appearing, it is built by robots, you get warnings when you have not enough items to build i...
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