Hi!
I thought to leave the original modules' items and recipes intact to not mess up the normal balance of the game. But I did notice that most machines in the game don't use module categories but module effects to filter stuff. So if I messed with the categories on machines it might be not that mod compatible.
But I just had the idea to turn the vanilla modules into items that don't count as modules. That way I don't mess with the categories AND they don't clutter your UI.
In the meanwhile, you can just ignore the old modules and use the rainbow modules in the silo to get module effects
:D
PS: The change to old modules so they don't have any effect is optional. You can turn their effects back on in the mod settings menu! I made it like that so everyone can play how they most enjoy the game :)