Thunderbolt-3 support is very early in development under Win10.
Right now, only MOTU has true "PCIe via Thunderbolt" drivers available (for the larger AVB units).
Thunderbolt-3 is working fine... but you've got to have all the above in place:
- Running one of the latest Z170x or X99p chipset motherboards that provide Thunderbolt 3 via USB-C port
- Win10 up-to-date
- Thunderbolt-3 (USB-C) to Thunderbolt-2 adapter
- MOTU AVB audio interface with Thunderbolt port
If I were getting a Skylake motherboard with Thunderbolt-3, it would be neither of the above.
Thunderbolt provides access to the PCIe bus. Nothing more... nothing less
You (of course) have PCIe slots in a modern machine... if you need to run ultra low round-trip latency.
Thunderbolt will not out-perform PCIe. Under the best of circumstances, performance will be similar.