but, if the patents are only on the long-filename extensions, where is the stick to back up the carrot? what basis would microsoft have to sue a camera maker who is not infringing those patents, should they choose not to license FAT?

I'm guessing here, having not read the patents or the M$ page, but even if there's no patent to cover FAT, the FAT code or FAT structure itself could still be copyrighted. You don't necessarily need a patent claim to back up a license, a copyright is sufficient.