I'm watching this again (how can you not? ) and am noticing a lot of clever things done with the Koopa shells as pitched samples, and the actual natural tempo of certain sound effects such as the Yoshi-mounting sound. And contrary to what was said, the sound effects very often do actually match the pitch of the music, for example the music blocks in the section starting at 4:50 (beautiful song, btw...wish I knew the source). And it's not just "emphasizing the beat"...most of the melodies are played out in their entirety.
Anyway, just saying, this is like the Captain Falcon/Fire Emblem synch video x 100, and I didn't hear anybody complain about how lame that was. I guess there was the expectation that the level would actually play the correct pitches as well as the rhythms due to the misleading thread title, but c'mon guys, seriously now.