In some testing on a MacBook Pro with USB 3.0 and an earlier MacBook Pro with USB 2.0 (no USB 3.0) I've found
Both will boot to an external disk (a clone of the internal drive) if the drive is in a USB 2.0 case.
The USB 3.0 external case drive can be read by both machines. It does support USB 3.0 on the newer MacBook Pro.
The USB 3.0 drive is clearly an option in System Preferences, Startup Disk, and I can select the drive just fine.
The USB 3.0 drive will NOT boot on the newer MacBook (but it boots fine on the earlier MacBook with only USB 2.0). In fact, when booting holding down the option key, even then the external USB 3.0 drive is not visible on the newer MacBook, but is visible on earlier MacBook.
Once the OS is fully up and running, the USB 3.0 disk shows up fine as a device in Finder, it works at USB 3.0 speed, etc.
USB 3.0 is NOT supported by the internal firmware in the newest MacBook Pro so it cannot boot to the drive, but the Operating System itself clearly adds the support for the USB 3.0 device once it is loaded.
USB 3.0 is supported only in the operating system, and not in the firmware.
This makes the USB 3.0 support far less valuable, in my view, since booting to an external USB 3.0 device may be a very handy way to have a backup of the internal drive that can be used a reasonable speeds.
At this point, I have to put the external drive in a USB 2.0 enclosure. It boots, but offers absolutely no advantage on the newer MacBook with USB 3.0 support.
Perhaps we'll see an updated firmware that solves this problem.
My current Boot Rom Version is: MBP91.00D3.B08
I looked here: http://support.apple.com/downloads/#macnotebooks
but didn't find a description of this USB 3.0 boot issue (yet).