Can I make a directory on OS X appear as a volume so I can backup using Super Duper?
If you can share arbitrary folders on your Transporter you can then mount that folder across the network and SuperDuper will see it as a volume.

Failing that you may just want to create a disk image in that folder and have SuperDuper back up to that. That is how I do it with an external drive on a Mac that is always on. Several Macs back up to that drive, each to their own disk image via SuperDuper