The game you refer to is against So Fla, and that was in Kelly's second year. Ok, a simple mistake, but do you recall that the entire drive leading up to the fumble was practically all on the ground. They were gashing the defense with power runs between the tackles. The fumble was the result of a great strip as Jonas was about to score. That's not a play that supports your argument.
Kelly has had several years where they've had a strong running game. That has not been the issue. Rather it's having a diverse enough offense that the other team can't predict the play that's coming. And as it's been pointed out, their red zone offense has been pretty good in several years. Last year was not one of them.
As far as a fullback, ND used an H back last year. That's the modern equivalent of the old fullback of the 80s and 90s.