digimorf:
what I can't understand is why the bootloader inside the SAM3X8E, that should be SAMBA, appears to be BOSSA that is an opensource bootloader and shouldn't have nothing to deal with SAMBA.
When you install the Arduino IDE, you also install BOSSA. The USB VID and PID for SAMBA are registered as BOSSA on your computer. So when you connect the Due, SAMBA publishes the VID and PID and the computer matches that to BOSSA. Further, BOSSA has everything to do with SAMBA.
Doug