Why doesn't the master branch BOSSA work on Arduino Due?
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.