PFS3 is faster than SFS.
No comparison on my system. PFS destroyed SFS in my SysSpeed tests.
PFS3 doesn't generate massively fragmented files when two or more applications write files to disk. SFS does.
I can't verify this. SFS is slower and thrashes the HD more with simultaneous writes.
PFS3 performance doesn't deteriorate over time. SFS does.
This is my experience too. I wouldn't consider this is a major issue with SFS.
PFS3 has a repair tool. Often with SFS the only option is to copy data over, reformat and copy data back (MorphOS does have a SFSDoctor tool, however).
SFS has a recovery tool that works under AmigaOS 3. It's very buggy and slow but I used it to recover a partition. I did have to reformat.
The biggest issue with SFS is bugs.
Can't the mask force the buffer alignment to whatever is needed? I use MASK=0x7FFFFFFC to force longword alignment as that is faster.