This was always the trade-off with independence. We knew that we could have much better regular season schedules (as compared to G5 leagues), but our post-season access was limited (even worse than G5 access). Basically, undefeated or bust.
Notre Dame gets the benefit of the doubt, but their only high-quality game was their loss to Cincy. Their other wins were at best on par with BYU's.
It's not entirely ND's fault either, because their opponents were having down years. (FSU, Stanford, USC, Wisconsin, etc.)
The point is that the system favors P5 conference champions, even when the ACC and Pac 12 are only marginally better than the MWC or AAC, if at all.