In my games, Stone is usually the most heavily used resource. How come you have excess stone?

I don't understand how it would be the most heavily used. For what purpose? I mean if you have a use for all of it you can always just not use the added recipe here and be fine with that.

I use Space Exploration, Dectorio and Krastorio, so I need it for Glass, Silicon, Lithium, Concrete and rough pavement.

That makes sense in that environment, but this mod is not designed for use with those. Imperfection is intended to keep the game close to vanilla and specifically to not add in a lot of the complications that come with overhaul mods. It is very likely that going with such setups and adding Imperfection to it will break something.