This board does call out USB 3.0/3.1 separate of 2.0 and I can disable/enable them independently. I no longer have a Vive to test this with as I shipped it back to HTC and I have also already reinstalled Windows. Shortly after, I discovered that a 6TB archival drive in the machine (which was being written to during the last crash) was malfunctioning so checking/repairing it consumed the remainder of the evening. Thankfully, that's been repaired without issue or data loss.
If you need a guinea pig, I can certainly set up the system to do that however you'll need to provide a headset (which I'll provide a CC # for as a sign of good faith) however I didn't want to get stuck with the Vive and had a limited return window to send it back.