I was wondering why the Desinger has choosen to use a atmega16 in between the USB and the SAM. Whats its use? Does it toggle the erase flash pin to perform uploading? Would not it have been much better in speed and price to use the USB directly?
Yes it does assert the erase pin. Also I think it is a case of using proven technology to provide the USB interface.
The reason is very well explained by Paul Stoffregen here: