Wish I would have searched this properly last week! Good catch - I had a friend look into this and he actually found the why behind the fix.
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The USB 3 hub and devices are special. The USB 3.0 **controller** is connected to, and available on the PCI bus, which WinPE can see. That means, by default, WinPE will be able to see the controller. That means HIIClient can see the controller and find, download and add a driver for the USB 3.0 controller. That matches your results and the results of HII.
However, the USB 3.0 hub is on a special USB 3.0 bus. The bus is called NUSB3. WinPE **CANNOT** see the NUSB3 hub by default. That is because it is "behind" the USB3 controller. The USB3 controller runs the bus and all the USB 3 hubs and devices. That means it cannot be seen unless the USB3 controller has a driver installed and running. WinPE **DOES NOT** have a USB3 controller driver available by default. That means when HIIClient.exe asks WinPE what devices are connected, WinPE will not return information about the USB3 hub. Because there is no USB3 controller driver, the bus (and any devices connected to it) cannot be seen. WinPE will return only information about the USB3 controller, which is on the PCI bus.
If you get a Windows 7 32-bit USB3 **Controller** driver, and add it to WinPE, then when WinPE starts up, it will be able to load the driver for USB3 controller. Once that is loaded up, THEN WinPE can see the NUSB3 bus, and subsequenty the USB3 hub. Since WinPE can now see it, HIIClient will get that information, download the driver and it will be installed when Windows boots up.
Get a Windows 7 32-bit driver for the USB 3 Controller. Add it to WinPE, the same way you would add an MSD or NIC driver. There is button in the console. Once it is added to WInPE, update the WinPE image on the PXE representatives. Then run HIIClient again. If you added the correct USB3 controller driver, it will be able to see the hub and will download the drivers for both the hub and the controller.