While this is listed in the FAQ for the Caldiget Thunderbolt Station, I believe this applies to all thunderbolt devices:
12.
Can I connect an external USB 3.0 storage device to the Thunderbolt Station in order to boot my OS?
Yes, you can boot your OS from an external USB 3.0 drive connected directly to the Thunderbolt Station if you are using OS X 10.9.2 on a 2013 Mac or later.
I think the basic rule is that if the mac is equipped with USB 3, it can boot from a thunderbolt USB 3. Since the OP (and my personal) iMac is a 2011 thunderbolt model, it will not boot a USB 3 drive.
I am using a separate thunderbolt drive to boot from (a Delock thunderbolt enclosure) and it works great for my 2011 iMac.