Nah, I believe that the tempo is indeed the same across both versions, but they play fewer notes (and hold them longer) in the underwater variation. But since the tempo's the same, they're all in sync. I (or even better, Rasmusic) should overlap both versions some time to show how they sync up
BTW, I think a raw excerpt of this (and some other) variation got released by IGN some time ago. That was a single track with like 3 channel fades.