I own an '01 which is a completely different car, but the following principal or theory remains the same.... It is likely heat generated from the exhaust, which is routed very near to the transmission tunnel. My car does not have any sort of heat shield between the exhaust and trans tunnel sheetmetal, not sure on the 05-09 cars. May be worth sliding under the car for a look at things, but from what you describe it sounds pretty normal. Obviously if you have melting carpet or something like that then that's a problem but otherwise I wouldn't be very concerned.

 

When I had that problem on my fastback, I wrapped that section of the exhaust in header wrap and the problem was solved.