I have an Elite EL token. and I have some tools to work with it. One of the softwares is Elite EL set mode. As you see I have two options, HID-Mode and USB-Mode.
Q : What is the difference?
From my expereince, the difference is really only for determining the difference of connection between USB and older Serial and Parallel connections. HID stands for Human Interface Device, if you were wondering. In this mode, the dongle will function as if it is connected to your computer via a Serial port (or other similar olden-days connections), and if it is in USB mode it will function as if the device is connected via USB.
Hope this helped.