Is it o.k to have the sys: partition use PFS or SFS or should your sys: always use the vanilla filesystem?
SYS: can be PFS3 just fine. It even works with MorphOS (on Pegasos and Efika, on Mac the partitioning system doesn't support external filesystems). Note however that it doesn't work with AmigaOS4.
SYS: SFS works on all systems.