Are Mallow and Geno unique to Super Mario RPG?

Mallow himself doesn't appear in any other games, but minor characters occasionally pop up who look like they might be from his species. Geno (or at least the doll he inhabited) had a cameo explaining one of the minigames in Mario & Luigi: Superstar Saga.

The most popular theory behind their rarity is that Square-Enix kept the rights to the original characters in Super Mario RPG, and generally does not allow Nintendo to use them again. This has never been officially confirmed one way or the other, but worth noting is that the end credits of M&L:SS do list Geno as belonging to Square-Enix. This confirms that Squeenix does indeed own those characters, and Nintendo really does have to get permission. But on the other hand, Nintendo got permission, at least for this case. Had Squeenix been refusing this whole time, and only relented this once? Or has Nintendo just never asked before? Nobody outside these companies is sure, and the people in a position to know aren't telling.