You don't need MS-DOS to use an MS-DOS boot sector, so it's not really "depending on microsoft" here. The point is, up to now they've worked portably. Linux and Windows and OSX(it has to, to understand standard USB flash drives) and a big variety of off-the-shelf tools like Partition Magic can understand them. Abandon that de-facto standard and suddenly, you're left to your own devices. I believe there's features in the NTFS filesystem itself to overcome this but obviously this isn't much help to other operating systems.