tl;dr: I built a system with the v1.1 board and tested it with a TB3 device; it didn't work. Hope my update to this thread helps other SFF-heads.
Thunderbolt device with USB-C connector showed up in Device Manager, but only as a USB "billboard" device. Gigabyte, if you're listening, some of us want Thunderbolt on mini-ITX. Actually those of us with SFF need Thunderbolt the most!
I ordered the GA-Z170N Gaming 5 from Newegg in Nov 2016. It was advertised as v1.0 on the site and receipt; the box and motherboard that arrived were v1.1. Had Killer NIC 2400 instead of 2200 which seems to be the only difference.
Gigabyte's Support/Downloads page for this board has a "Thunderbolt Driver" software download. This installed fine on my Win10 Pro system as "Intel Thunderbolt (TM) Software." Figured it wasn't needed but wouldn't hurt to have it. CPU is an i7-6700K. BIOS is F5; I see they updated to F20 but it makes no mention of Thunderbolt support.
I tested with the only TB3 device I have, an Apple Thunderbolt3-to-Thunderbolt2 adapter, and plugged it into the motherboard's USB-C port.
* Win10 displayed a popup: "Try improving the USB connection / Make sure the device you are connecting to is supported and you are using the right cable."
* The adapter appeared in Device Manager > Universal Serial Bus Devices > "Thunderbolt 3 (USB-C) to Thunderbolt 2 Adapter".
* Properties > Details > Device description: Billboard Device (Google this but it's basically a USB-C Alternate Mode device going into a "no this protocol isn't supported" state by masquerading as a USB device... kinda elegant failure mode. Keep in mind that Alternate Mode may specify DisplayPort, Thunderbolt, etc. so this is a sure sign of it not being supported by the mobo.)
* Properties > Details > Hardware Ids: VID 05AC, PID 1657, REV 0348. Vendor ID 05ac is Apple, so the billboard device enumerates to the correct vendor.
* The Intel Thunderbolt software launches but does not recognize anything.
I figure that if this motherboard actually has Alpine Ridge, Gigabyte might still need to pay a licensing fee to Intel and/or design in specific Thunderbolt 3 support. Ah well. Still a great board, but TB3 would have been nice.