I think most people, including the people at Square, would be fine with mods that are just visual enhancements... But as Yoshi himself said, they have no reasonable way to see what people have installed or active, and with no proper way to add them other than actually modifying the client itself it puts everything into a messy situation as they don't want people poking into the game's files and injecting things...

I think the most reasonable thing they could do to try allowing some would be making a whitelist, and everything not on said list being prohibited.