What changes is someone else takes the responsibility. If all goes south, Nintendo can sue for damages and claim gigantic amounts of money. It’s difficult to deal with that responsibility using a community that is focused on writing stories about magical princesses.
Nintendo or Japanese companies generally don’t do that. There is a huge market (doujinshi) of selling fan-made manga for decades and it is generally seen as a tradition.
While true, Nintendo in particular is known to be particularly bad with this topic unfortunately, to the point of demanding that people who host Lets Plays on Youtube to take their videos down.
