The 2060 and 4060 SCSI driver is broken by default, and only looks for filesystems in the KS ROM. You are stuck booting from FFS partitions, other filesystems don't even show in the bootmenu. You can boot from SFS partitions if SFS is stuck in a custom ROM (at least I did on my 2060).
Fortunately, Doobrey was kind enough to tackle the problem. You'll have to burn and install the fixed ROM(s) after running the patch. Been running the fix for a few years on my 2060, booting from PFS3 partitions.
I haven't had feedback yet on the 4060 fix, but presumably it works as both versions were riddled with the same bug.
Further details and patch available on Doobrey's site: http://www.doobreynet.co.uk/amiga.html