8.1 can go thunderbolt for sure but not sure about usb 3.0. Do the install on the main drive, winclone it in OSX to the TB drive. It should boot by holding down the option on power up to select the TB disk.
Perhaps it may work on the haswell designs with the usb 3.0 built into the chipset but I've not attempted one yet! Subsitute TB for USB 3.0 in the above instructions above and give it a try!