Thunderbolt is just a direct connection to the logic board. So yes.
Thunderbolt may have a very high bit rate, but it still requires protocol translation. So it's never quite as fast as SATA3 (6Gb/s), even though Thunderbolt is supposed to have a higher bit rate (10Gb/s). The protocol translation introduces a bit of latency, and it uses unnecessary power. I'm not saying TB is bad, just that it's not the same as direct PCI or SATA access.