If you're talking about a single hard drive, there's no speed advantage to using a Thunderbolt enclosure or even a USB-A one or USB-C one that implements USB 3.1 Gen 2. Hard drives are a lot slower than any form of USB 3 – whether you're talking about USB 3 carried on a USB-A connector, or on a USB-C one. In other words is the throughput speed to the HD faster than USB-C? That said is there any benefit in needing Thunderbolt/USB-C over USB-3 to run an external hard drive.
I understand the differences between those two in their similarities and differences.