1) When you compare apples to apples, Notre Dame played 12 regular season games, as did Georgia, Ohio State and Oklahoma. Notre Dame was the only team to run through its schedule undefeated, a schedule that was comparable in strength (Sagarin) to Ohio State's and Oklahoma's, and only marginally weaker than Georgia's.
2) Ohio State and Oklahoma, at least one of which is almost certainly going to be left out, are undoubtedly going to use the argument that Notre Dame did not play in a conference championship game, much less win one. See 1) above. You can only use conference championships (or at least should only use them) to compare conference champions to other conference champions.
3) Precedent has been set in regard to a "13th data point," as Ohio State and Alabama both made the playoff without even winning their divisions, and played only 12 games.
There is absolutely, positively no way Notre Dame is left out.