Well, that depends on the purpose of the clone backup. If you want offsite storage with it, then yes, it needs to be separate from TM. If, however, you just want a bootable backup, it can be on the same drive. That's what I do, and I use an online backup for my offsite. But everyone has their own preference on that end.
One correction, though. I do NOT recommend putting the Time Machine backup on one partition and the SuperDuper clone on another partition. Put them on the same partition. That's the most efficient way.