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?
No Arduino did not alter the chip, custom chips are massively expensive. If they are using their own modified version of BOSSA, then there must be a reason for it, probably the support of Arduino's hardware platform. To find out what the difference is, you have to find the code base used for Due and the original version when the code was forked. Often in such cases a project like Arduino can provide a patch to the BOSSA project, and that patch may or may not be applied to the master tree. Only way to find out is to check the BOSSA project repository / bug reports and documentation.
