Voidcraft will not overwrite a prototype's allowed module categories, if they are defined. It seems that the issue is that other mods create their own module categories and then don't do anything to ensure that crafting machines can actually accept them, and instead (incorrectly) assume that the vanilla behavior of accepting every module will hold. Objectively speaking, this is a problem with those other mods, not Voidcraft.
However, given how widespread the issue is, I've tried to do what I can. I added a setting called "Automatic module categories" that makes every module (except Voidcraft's own) usable in every non-Voidcraft entity. This should solve the issue you're having. It might break compatibility with other mods for other people, because it can't really know what other mods that create modules intend to do with them, which is why it's an optional setting.