Doesn't hurt 'em that much. As long as they continue winning, I don't see how they don't finish the regular season at #1.
I'm comparing this to last season. In the event that there are not two undefeated teams (as happened, IMPROBABLY, last year), the teams with the best loss and best wins get advanced. Last year, that was Alabama with A&M. Having the best wins jumps you up, like having Michigan, LSU, and Georgia.
Of course, finishing the season undefeated is a stopgap against putting your destiny in other team's hands.