Does it matter? Legal housekeeping is something corporations do all the time. In this case, they might want less friction with Nintendo. Mayhaps they also want to go full into protecting emulation, but can't do that if any ROMs are specifically part and parcel of a game.

It probably needs to be generic, like bro: you can't prevent the user from reading those files using an application, because those files could have been gained using legal methods. But it becomes harder to defend it in court if there are games in the Valve Steam store that specially target certain IP's directly.

So forget Mario and Metroid Prime mods, you'll have to get those working through an emulator that supports modding or add-ons.

In any case, Nintendo is reselling pirated ROM's because they lost their copy, so yeah. They can't ever be directly against ROMs, as long as they have been obtained legally ***