When using the same disk type with only accessing one disk USB 3 is abut the same as Thunderbolt
In other words, in this specific case the speed difference will not be down to USB3 vs. Thunderbolt but will be down to 7200rpm vs. 5400rpm. The 7200rpm drive will be faster in either USB3 or Thunderbolt.
However you are not comparing like with like, not only are you mixing interfaces, you are also mixing speeds, and you are mixing RAID vs. non-RAID. This makes a fair comparison almost impossible. I would say that if you configured the WD 6TB My Book Thunderbolt as a RAID0 stripe it would be faster, if you configured it as a RAID1 mirror it would be slower.
This would be a closer match to the Fantom - http://www.amazon.com/Studio-Desktop-External-Drive-WDBHML0040HAL-NESN/dp/B00F0J XE04/ but they do not say what speed drive it contains.