It's most likely that Mallow and Geno, while owned by Square-Enix(or even are co-owned), are on a "deal basis" where they are only used in conjunction with Nintendo's approval(as well as SE's approval, if more co-owned specifically). Didn't one of them not hit the US shore either? Besides, considering how hard it was to get it on the VC, it's pretty clear the actual SMRPG originals are just a pain to deal with on both ends. We just lack true details.
Also, usually any music in a Square-Enix game isn't owned by SE itself but the composer. So that likely is why it was able to get in. It's also unclear who actually owns the music since Nintendo was involved with SMRPG, though is usually hands-off for most franchises they license a game out of. Nintendo doesn't work the same way as SE does with music ownership(most companies don't, really), sooooooooo it's likely even more complicated.
It's kind of the unfortunate part about SMRPG. If it was a standalone game, it wouldn't be so awkward. But it's clearly Nintendo's core IP, they just don't have ownership fully of every piece of it. In a way, you could attribute it to being like a Crossover. Square-Enix owns certain bits and Nintendo owns certain bits. A crude comparison, but it somewhat fits the way the licensing is easier to look at.
