I have downloaded BOSSA for Linux, and have run
bossash->scan. I have also tried erasing and resetting the board before scanning. It does not work. According to the Arduino website, the native USB port is connected directly to the chip.
Isn't the master branch BOSSA (Arduino IDE uses it's own modified version of BOSSA) working because of a problem with this specific board, or have Arduino modified something inside the chip which alters the behaviour of the native port?