As others have noted, an internal drive can work fine as a Time Machine drive. Whether it's a good idea or not depends largely on your intended use. If you're using Time Machine as your sole backup, you're exposing yourself to additional risk - PSU issues can easily fry both internal drives, controller problems could fry both, etc. Is it a huge additional risk? No, but it is more than if your backup drive is an external one with an independent power supply. It largely depends on how much you value your data and how much that added protection is worth to you.
I think there are some definite advantages to using two backup drives - one for Time Machine, one for SuperDuper/CCC. That way not only do you have double redundancy, you get the version-backup functionality of Time Machine, and the bootable functionality of SuperDuper/CCC. Given how cheap disks are these days, it's a good option to consider. Have the TM drive internal for maximum speed, and you can have an external SuperDuper/CCC drive do nightly backups. For even more security, add a 2nd SuperDuper/CCC drive and rotate them offsite (work, friends/relatives house) to protect against theft/fire/etc.