I was trying to bind Y to special to see if it would help me chain waveshines rather than jumping from X to B repeatedly, but even though Y was only bound to special, it was inputting both jump and special. Needless to say, this did not help with waveshines.
I later unbound it from special as well, and even completely unbound it still jumped. Nothing is bound to the shorthop or fullhop specific bindings, and the Y button allowed me to do either, so it was a regular jump input.