Yea, I have one the last 2012's built which has all the supposed MT 82 changes and the same transmission as yours. It has made mechanical whirring noises (kind of like a blender) in the lower gears since day one. If the window is down or the radio or a/c on, it really can't be heard. Except for the typical 2nd gear cold notch, it shifts fine.
Update--took it to the dealer and let the service advisor listen. He didn't think it was problematic but suggested that I put about 1500 miles on the clock and come back if it still was bothersome (I had about 400 miles on the car when I took it to the dealer). The transmission is much smoother than my '11 GT even though it's noisy. No whine yet (except from the owner). If it doesn't get worse, I'll resign myself to living with it.
2013 Deep Impact Blue GT Premium, MT82, Comfort,
Electronics, 3.73 gears, Ford Racing Strut Brace,
Boss 302S 19" wheels,
255-40-19 Michelin Pilot Super Sports,
Bama 91 Octane Race Tune