I figured Spamalot had done that to make fun of shows like Phantom that are pretty much written with three different set of tunes to different lyrics-I know I'm exaggerating, but they probably did this in Spamalot to sort of mirror those shows. I agree that Piazza would probably not have gotten the Best Lyrics Tony were the two awards separated, I mean I always have issues with the lyrics for the opening sequence, they don't seem half as complex as the music.
I also believe that Avenue Q got the award mostly for its lyrics but I think the lyrics highly depend on the musical pattern so that's probably the major reason why this award is combined as best score; it is important to note that in early 1970s-don't remember the exact year but either 1970 or 1971-the award was divided in Best Lyrics and Best Music and Mr.Sondheim got both awards for Company, which he deserved of course.
I think that Schwartz probably did deserve a Tony for the music of the Wicked score but like Caroline-Q noted, there were other shows like Caroline... that had a more complex music score. I think the only Schwartz score that ever presented a competition to other Best Score nominees was Pippin and well, we all know Sondheim took the award home that year for writing what people think is his most "hummable" score-A Little Night Music.
"Some people can thrive and bloom living life in a living room, that's perfect for some people of one hundred and five. But I at least gotta try, when I think of all the sights that I gotta see, all the places I gotta play, all the things that I gotta be at"