I do wish that they would have included data on the exact measurement setup. IR thermometers are affected by surface material characteristics and can be affected by orientation and distance to the DUT. Thermocouples would provide the most reliable measurements. Barring that, we've always resorted to applying black non-reflective masking tape to the spot to be measured in order to eliminate surface effects. The next step is to ensure that the thermometer is normal to the surface and that all measurements are taken from the same distance.
It is likely that some of the extra heating is coming from the display. This post covers it:
http://news.ycombinator.com/item?id=3740270
There's probably nothing seriously wrong with it new iPad though. People probably aren't used to having a processor that gets hotter with usage so close to their hands. I have multiple laptops that get to hot to be on your lap. This is nothing new.