To answer your most important question, yes it's distance in the air, rather than distance gained by the play. I think you'd be surprised at the results. ND threw less passes <0 and 0-4 than Alabama and Stanford. In fact, ND was towards the bottom in those two categories.
ND: 11% and 14%
Stanford (with Hogan): 26% and 29%
Alabama: 15% and 29%
Oklahoma: 20% and 22%
I should also note that Alabama had although they didn't throw deep often, Alabama had very high success rates when they did. Also, Golson was pretty good on intermediate passes 5-15 yards, struggled 15-19, but was pretty good 20-24. I'm not sure what that means, although i'm not surprised at his <0 numbers as he missed on a lot of screens last year.
One large caveat is that the sample sizes varies for the different teams. ND's data only includes five games, while Alabama's includes 12 and Stanford's includes 10.