Even if the Big12 has an outright "champion", they should still be penalized for not playing 13 games. Same as ND.
The SEC, ACC, B10, PAC12 play a 13th game against ranked opponents.
I agree to a very limited extent that not playing a conference championship game should matter some. If you don't have that extra test, it should matter.
But, just the number of games by itself should mean very little. For instance, if Alabama didn't play in the SECCG, they still would have the toughest schedule of a contender. The idea of saying: "oh they didn't play an extra game", even if the games you did play were tougher by comparison, is a bit pointless. I don't care if Boise State plays 15 games, if they play them against crap competition they mean nothing to me.
To give an example, in 1996 BYU played 15 games. They actually won 14. They even played a few decent teams, but the bulk of their schedule consisted of WAC teams, so what did those wins really count for? In the same way I don't like people just automatically saying that the number of conference games matters, I don't want people saying conference championship games in and of themselves should be a huge factor. A factor, yes... but look at who a team actually plays before making a judgement.