The other "original" musical (as in not a revival) that made the Grammy cut is Shrek: The Musical, which is gorgeously produced, with a lush, full sound, great character performances and very nice packaging. Its sense of humor will play well for voters who did not see the show that goes with it (knowing the movie will help them understand anyway). And who doesn't love a funny fart song, especially when the sound engineers make them go from ear to ear?
And just as it lost the Best Revival Tony, so too will the recording of the new West Side Story, more than likely lose the Grammy. Despite the fact that the recording closely replicates the original in such stunning quality, and in spite of equally stunning performances across the board, the recording, like the show may suffer from what has divided audiences since it opened (and until more changes were made) and that is the inclusion of Spanish lyrics for the Sharks, most notably in "I Feel Pretty" and "A Boy Like That/I Have a Love." It probably won't matter that this recording is superb in every way.
Finally, I have not heard (or seen) the cast recording of the 30th Anniversary of Ain't Misbehavin', the Fats Waller revue that won the 1978 Tony for Best Musical. I can only guess at why it was included on the list. This version features two American Idol folk, Reuben Studdard and Frenchie Davis. One can imagine that that has something to do with its inclusion on an otherwise Broadway-centric roster of nominees. And I can surmise that the nod has something to do with the "committee" wanting the country to know that theatre exists outside of New York City. Most years there is at least one non-main stem or non-off-Broadway recording on the list. Fair is fair, I guess.