Not defending the patent for FAT - nobody prohibits device OEMs shipping a piece of software that manages data on the device without requiring the FAT to be present.
Those devices will offer a more complicated experience because they have to do something Microsoft doesn't have to because they have the desktop OS monopoly creating a competitive burden to everyone else. Looks like leveraging a monopoly on one market to gain advantages on another to me, even if it is a subtle way.
All they have to do to leverage their desktop-related monopolies is to sit tight and do nothing. And that's why it's really bad.
It worked out for Apple/iTunes just fine. I don't like this approach (and do not buy i-devices for that reason), but it is quite viable if executed right.