Is the MFT even documented and available via APIs on Windows? Could NTFS (at the expense of losing backwards compatibility in the file system (which already only extends to features that have been there before)) just change how the MFT works transparently for well-behaved applications (i.e. those that do not grovel around in undocumented data structures)? Admittedly, there may still be a number of applications that decide to »optimize« a system by digging around in parts that they have reverse engineered, and those might simply corrupt the file system when running on a newer NTFS version, but I guess that problem may have existed previously as well.