Ok here is the thing.
If its an early generation like iPod 1-5 (5 being "iPod with Video") the B&M sometimes reads the disk via USB directly, which means it may have to be Winblows formatted. If its a touch, iPhone, or something built recently, it uses a protocol to talk to the iPod/iPhone and so the format on the devices disk makes no difference at all.
At least that's how I understand it.