I've made Amiga CF/SD/HD drives under MorphOS many times. It's really pleasure to unpack complete WHDLoad collections etc on fast machine. And of course MorphOS also preserves Amiga's protection bits and all. So, it's perfect solution :)

What I've done is to separate MorphOS native and 68k filesystem versions. I install 68k filesystems to cards/drives with different identifier so that they won't get mixed. For example when native SFS is SFS/00, I install 68k SFS to disk's RDB as, lets say, SFS/03. Then it's sure that 68k filesystem is used on both MorphOS and real Amiga for that media. Then you don't have to worry if MorphOS native filesystem is compatible for everything or not.

And I do all partitioning etc on MorphOS, just plug the ready card to real Amiga and no need to tune anything on it.

BTW. PFS3DS didn't work here on USB.. probably direct scsi commands don't go through USB correctly. But standard PFS3 and SFS etc have worked just fine.