I have a thread already posted on this in the general 2011+ discussion. What all the other guys are saying about the S and R being dedicated race cars is true. The T6060 has it's issues with shifting in the GT500, believe me.
Ill post this one more time, and I have been backed by a good source, the T6060 is used because it is better designed for the race environment (in the most simplest way, YES, the T6060 is stronger than the MT82). The MT82 is used on the street cars because it is a nicer geared/shifting transmission. That is the trade off Ford made between using the MT82 instead of the T6060. You can believe differently about the nice shifting of the MT82, but it has been beat to death by people and there is no need to continue that discussion here.
2012 Ingot Silver Mustang - 3.7L V6, Performance Package (traded)
2012 HP White Mustang GT - 5.0L, Premium, 3.73 rear end