I have spoken with 2 different manufacturers of AFCI CB. The temperature difference from the standard CB to the AFCI CB is the electronics installed in the CB. They are changing the miliamp requirement of the electronics as the technology has improved, and the AFCI CBs that are to be marketed by the fall of 2007 will run cooler, yet still a little warmer than a standard CB. The heat of stacking the current type is of little consequence even now.
I am not a fan of the AFCI breakers yet, but there are issues with installation practices of wiring methods that these devices are bringing to the forefront... that is the poor wiring practices that some out there are performing and blaming on the AFCI tripping. I am not saying there are not issues with the current AFCI, but I (from inspecting) believe that there are issues with the wiring practices that these units do expose.