From what I understand, early versions of the Disk Controller II required that there never be two or more consecutive bit times without a phase transition (which would read as "0") but an upgrade to the "Woz machine" controller PROM made it possible to accommodate bit patterns that had two consecutive zeroes. This made it possible for the controller to read FM, MFM, GCR-encoded data, but software designed for the earlier PROM would work as-is with the newer one.
The boot PROM of the Disk II was changed, however, so that instead of trying to read a boot sector written using the old format, it would instead load a boot sector written in the newer format. This makes it awkward to use with the new controller boot disks designed for the old controller.
Would there have been any technical obstacle to having DOS 3.3 disks include an MFM-formatted boot sector, thus avoiding any need to make newer versions of the Disk II incompatible with the old ones? I would think that from a usability perspective, even if making a disk bootable would require use of the "MASTER" program [which is necessary if one wants a disk to be bootable on machines with varying amounts of RAM], use of such a program would have allowed users to select whether they wanted to install a minimal-RAM version of DOS which was slow and could only handle GCR disks and lacked text file read/write support, a larger version which added text-file support and included some extra lookup tables to allow better performance, or a full-featured version that could process both MFM and GCR disks interchangeably. Having an attempt to boot an incompatible disk stop with a suitable message would be much nicer than having the drive spin forever until it wears the boot track off the disk.