As another poster mentioned earlier in this thread: Leap of Faith received a Best Musical nominations simply because it received more votes than the others. Now, we can theorize why each voter voted the way they did( some thought it would tour, some wanted to honor a musical currently open, some genuinely liked it more than the others), but it's not as if the entire committee sat in a room and conspired to vote for the one best suited to tour.
As far as nominations in the other categories, there were simply many more deserving options to choose from (than the limited number of shows eligible for Best Musical) and the voters chose the other options.
Leap of Faith being nominated for Best Musical and nothing else is odd for sure, but the probable reasons why it happened seem rather simple to me.
By the way, I think the nominators largely nailed it this year. So happy for Osnes, the way the score category turned out, and the large nomination tallies for Once, P&B, Newsies, and Nice Work. Can't wait for the telecast.
"...and in a bed."