However, finishing 12-1 vs 13-0 may have an impact on how highly you start ranked in the pre-season polls the next year. Especially if you get destroyed in the semi-final game...

And before anyone says anything about how the CFP won't use the polls you have to ask yourself seriously if you truly believe the polls won't have an influence on the humans on the committee doing their own ranking (i.e. 13 person poll)....