Lens image stabilization is not taken into account.
I think I may need to re-test this on my 1D X. From previous testing, IS didn't matter on the 7D or 5DII, but I just looked at a shot in Av mode with Auto ISO, and using the 70-200mm f/2.8L IS II at 200mm, the camera selected 1/60 s and ISO 125, and similarly a shot with the 100-400mm at 400mm had 1/125 s and ISO 320. Both are well below 1/focal length.
So...now, I'm not sure if the lower limit is just picked differently on the 1D X, differently on cameras which allow a min shutter speed in Av selection, or is actually taking IS into account.