Well, it's certainly your choice to see it that way. But they had five slots to give, and I think they filled them with what they thought were the five best performances.
Radcliffe just didn't measure up, in their opinion (and in mine, as well). Maybe he was #6. Does that offer consolation?
You are 100% right that the show was a ridiculous cartoon. That's exactly what it is trying to be. How smart of you to figure it out. As to Tony Shelton not deserving a nomination, well, if YOU didn't like his performance then yes, definitely he shouldn't have been. Never mind the thousands who cheer his performance including nearly ever critic who reviewed the show.
I would have nominated both Tveit and Radcliffe before I nominated the two leads in Mormon who will easily be replaced, as good as they are. I hated Broderick in the last revival but the whole production was a disappointment. This current revival of How to Succeed is so much better.