That's not a glitch.
Sephiroth and Vincent share the same space in the character data map. The moment you name Vincent, Sephiroth's data is overwritten. You'd need another character to act as Sephiroth, or disable the field script that swaps the two chars.
As for playing with Sephiroth - you're going to have to disable his main AI script in the KERNEL, else you won't be able to control him.
Using Supernova as a limit? I'm pretty sure enemy attack animations are out of range for limit animation indexes, though that wouldn't stop you assigning a spell as a limit in the KERNEL (I'm not sure how reliable this is). But it's moot as the animation requires the 'swirling heavens' background to work, anyway. There's the Japanese supernova animation data on non-JP versions, which is supposed to be background-agnostic, but I'm not sure how to restore it.