How many future NFL players did Clemson face compared to Alabama, especially in the trenches?
That will provide your answer.
YES Alabama was more tired going into the playoffs and especially coming out of the semi-final game than Clemson was. It made a huge difference, although it was not the only reason Clemson won. Clemson does not need to ever apologize for this; no one is going to take the trophy away unless the ncaa does for some stupid reason years down the road. The month off leading up to the playoffs is not enough time to completely heal from the season long grind. It helps a great deal, but you're not 100% going into those playoff/bowl games. And then you play that semi-final against another great team and it takes you down another couple of notches.
Clemson did not play another great team in the Cotton Bowl. And again, Clemson owes no one an apology for that. But to gloss over it is to be obtuse.