I modified the startup sequence with :
SYS:C/LoadModule L:Fastfilesystem L:RAM-Handler L:Shell-Seg DEVS:scsi.device LIBS:workbench.library NOREBOOT REVERSE
SYS:C/Setpatch SKIPROMMODULES fs,icon,ram,scsi.device,shell,workbench QUIET
as prompted by the installer and I get an Amigados "Unknown command" error.
I put it at the beginning of the startup sequence file and deleted the existing Setpatch command, but I appear to have broken something as Workbench will not load.