There has to be some other factors. Riding last month in 35 degree weather at highway speed (well, my highway speed), I realized the front cylinder was and header pipe was experiencing probably a minus 30 degree wind chill, and the much less. So, depending on how fast you stopped to get the reading, there could be more variables. I think the exhaust could be hotter than "the engine" because the exhaust was just exploding/burning and the admittedly sharp curve of the pipe is going have more dwell time of heat passing over it than a flat surface. Just my thoughts.
What I was really wondering on the bike in that cold weather is what is harder on the bike: is the bike hotter at 80 mph at 35 degrees (if, of course, one could find a legal place to drive that speed) or 60 mph and 90 degrees?