(Custom Build) Super Time Capsule - am I missing something
I don't think you need to have one folder per workstation - each backup will be created in a .sparsebundle file, that is mounted by the remote workstation that belongs to it, and used as the backup disk.

At home I have a Mac Mini running OS X Server, and I also back up my MacBook Pro and my wife's MacBook Pro to it over WiFi. It works well, and apart from the size of the disk I imagine it would scale just fine.