The disk physical format and filesystem are separate things. OFS or FFS filesystem can live on various different physical block devices (but for amiga to read/write them, there must be a way to access the disk via exec device driver. Example of FFS on custom formats is
diskspare.device).
Typically games used different physical disk format to achieve couple of things: a) copy protection b) store more data on the floppy. Using custom physical format usually also meant using custom filesystem, since the OS couldn't do the floppy access then, anyway. There are probably dozens of different custom filesystems, but less different physical formats (not all of them make sense).
The first track on the floppy always is in the standard 11-sectors-per-track MFM-format so that the OS can load the bootblock. The bootblock (2 first sectors, 1KB) itself is executed, and it typically loads some more blocks from the first track, which also include the custom track loader routines. These routines are used to load the actual game off the custom format tracks. Usually there's also 2nd set of trackroutines inside the game itself.
Here's some interesting information about standard physical floppy format and OFS/FFS:
http://lclevy.free.fr/adflib/adf_info.htmlMore interesting stuff here:
http://zakalwe.fi/~shd/amiga-cracking/
