There is nothing like "Rockbox-bootable". The Ipod boots off a special firmware partition (using the partition type 0, so it won't show up in Explorer). To make Rockbox run you need to have (a) the bootloader installed, that goes to the aforementioned firmware partition and (b) the main build, which goes to the data partition. Booting, however, is done by the bootloader, so strictly speaking you don't need to do anything to the data partition to boot. However, without the main build you can't run Rockbox.
And as a side note: depending on your OS you don't need special tools. mkfs.vfat on Linux can create the filesystem just fine. Windows refuses to create FAT filesystems larger than 32GB, but that's Windows-specific.