No doubt they underperformed at ND. But their position coach has them prepared enough that the NFL came calling, so he must be doing something right. Maybe it's not the position coach, but the play caller?
I think it's a combination of both things. Niklas was drafted because he was a physical specimen... I'm also now convinced that Koyack was drafted "because ND TE."
I think the TE's need to be given more of an opportunity, and part of that seems to be because the current "true" TE's aren't living up to the billing as in-line blockers that can also catch the ball... if they stood out as true weapons, they'd get their chances.
At the same time, BK has never actually had/used a true stud TE in the traditional sense aside from Eifert, and the argument could be made that he wasn't a true TE and that BK lucked into having him as a weapon. Niklas was close, but BK didn't really feature him. His best TE at UC was Ben Gidugli, who was essentially a jumbo WR that patrolled the seams.
I'm just rambling now, but I'm trying to say that we've kind of been duped into believing ND as TE-U, and it's because of both coaching and game planning, draft history be damned.