Louis,
I have two systems with USB 3.1. I believe they are both Gen 2. One is a combination Thunderbolt3/USB-C port. The second has separate USB 3.1ports plus Thunderbolt3. I can see the Intel USB 3.1 eXtensible Host Controller listed on both but there is no USB 3.1 Root Hub. Here is a screenshot of Device Manager for the second one.
It also shows the one external drive I have connected to one of the 3.1 hubs.
Why your 3.1 controller is not showing is strange. You might want to try something like HWInfo to see if the controller shows up there.
JohnD