Admittedly, this is a little beyond the scope of my knowledge to explain in great detail but, essentially:
USB type C is the port shape & layout - whereas Thunderbolt 3.0 is (one) technology that can utilize the port.
At a glance, all type-C ports will look fundementally the same, but it's what's 'inside' that counts.
It's bringing consistency, with the plan for a single port.
USB went from type A, then type B (and variants - miniUSB, microUSB etc) and now to Type-C.
Thunderbolt used mini DisplayPort for Gen 1 & 2, and now agreeing to use the common Type-C for implementation going forward.
USB Type-C brings reversible orientation to the table, and not much else.
What's inside.......
USB3.1 or 3.1 (gen 2)) as an option - limiting...