With USB 3.0 a new bus was created. Instead of being on the PCI bus it is on a new bus. Depending on the manufacturer, that bus can be defined differently.
The reason HII doesn't add the usb drivers is because it cannot see the usb child devices because the bus does not have a driver loaded. You need to add the USB 3.0 drivers to WinPE. If you run Devcon.exe from Microsoft to view the hardware that WinPE can see you will only see the parent usb device. You will not see the child devices. HII will inject the driver for the parent device, but since it cannot see the children, it injects no driver. Once the parent driver is in WinPE, the child devices will be visible and HII will be able to add the drivers for the children.