I get your point. Personally I don't see an issue with visual mods. However Sqex is Japanese and they tend to be really strict when it comes to that sort of stuff. Look at Sony, Nintendo, Bandai Namco, Konami and so on. Maybe it's to do with their laws or something. You mite not be allowed to altar someone's code over there.

To Sqex defence, if someone downloads a virus from a mod and they say mods are allowed it could look bad on them. But then on the other hand they could make a launcher that has a mod browser and mod loader included. The mods listed in the browser could be searched for viruses.

I can see why they mite not allow it even thou it would be better if they did.