I know it will boot from a Backup made from Carbon Copy Cloner. Will the iMac also boot as well from a Thunderbolt drive?
What are the Pros and Cons of each setup?
A clone to a Firewire 400 or 800 or USB 2.0 or 3.0 or Thunderbolt equipped external HDD will be as bootable as a Mac OS X install originally installed on such external HDD.
I know it will boot from a Backup made from Carbon Copy Cloner. Will the iMac also boot as well from a Thunderbolt drive?
What are the Pros and Cons of each setup?
I'm not quite sure I understand what you're asking, but I'll tell you what I've done. I attached an external Thunderbolt enclosure (Buffalo) with an SSD inside. I then started SuperDuper! and had it create a clone of my internal Fusion boot drive onto the Thunderbolt drive. I then restarted my Mac and depressed the Option key while booting. I selected the external Thunderbolt drive and booted from it. Is that what you're asking?
I have a Thunderbolt and USB 3.0 external enclosure, both with Samsung 840 Pro SSDs. The Thunderbolt drive (Buffalo) uses a bit less CPU overhead, and the USB 3.0 drive (Firmtech) is a bit faster - all using benchmarks. However, in simply using the drives I cannot tell any difference. In other words, if I hadn't actually LOOKED for differences I could not tell you which drive was faster or which used more CPU power. The biggest difference, IMO, is that Thunderbolt drives support TRIM for SSDs and USB 3.0 doesn't.