What are the contact pads near the ATmega32 chip on the Arduino Yun?
They look like the footprint for an alternative package, probably the TQFP-44 variant. Having both footprints: QFN (the leadless package that is installed) and the alternative TQFP variant allows a single board to be used depending on the availability of either part for more flexible BOM management. You could also use it for testing, as originally suggested as well.