I have the Hemi with eTorque. I leave my AC on Auto all the time. I leave the Start/Stop feature enabled all the time.
My AC works like I'd expect it to. When it's hot out, the AC fan is running full blast when I start the truck. It gradually slows down as the cabin cools off. I've never noticed it shutting off completely (which is not surprising, since I've only got 600 miles on the truck, had it for 10 days, and it's summer time here). It continues to blow even when I come to a stop and the engine auto shuts off.
I have never gotten any kind of transmission clunk, either.
The AC works pretty much just like the Auto AC in the '09 that I just traded in. The transmission is smoother than the 6-speed that was in my '09, as you'd expect.