Can you explain what storing it in the RDB means?
In HDToolbox, click on Partition Drive, then on Add/Update (in 3.1 HDToolbox you have to activate the "advanced options" checkbox for the Add/Update button to appear).
Then you see a list of file systems in the RDB of this disk. Here you can remove, add new or update existing ones. When you add one you have to enter an identifier (a.k.a. DosType). Do not leave the default, use the one mentioned in the installation instructions of the respective file system.
For more details read the manual of PFS3.
I had, I guess, always assumed that when partitioning the drive, it was doing as such.
HDToolbox automatically adds FastFileSystem to the disk. If you want to install a third-party file system like PFS3 or SFS, you always have to go through the manual process.
Just to clarify, you can boot from any sized device, its just the boot partition that needs to be in the 1st 4 Gig.
Yes, that's right. To be more precise: the boot partition must be accessible by the ROM driver. Once it starts to boot you can load additional/updated drivers from disk.