When I play Elite: Dangerous with DK2 and throttle/stick, I would tweak the position of the actual controllers on my desk so they matched the position of the virtual sticks in the game. The appearance of the virtual throttle/stick in the game is essentially a recreation of the actual model I have and the game is set up so the virtual hands move to mirror what I'm doing in real life.

Obviously with the current setup it doesn't detect my hands in real space so the on-screen motions only happen as I make them in real life but as long as I keep my hands on the controllers, the illusion is great. Move the stick a little to the right and the guy on screen, sitting in the same position does the same.

I think once they add a Leap/Kinect/RealSense type depth cam on the front of these HMDs you'll get some basic hand tracking for better representation. As the article says, it doesn't have to have the most realistic graphics if the feeling of actually seeing your "avatar" moving 1:1 with your actual motions flips some switch in your perception and it's easy to feel like the virtual person in the virtual environment is an extension of you in the real world.

I've played Elite: Dangerous a little bit and have been meaning to get a better control setup for it. The ship's cockpit has an amazing amount of depth to it. And I love how screens in your ship react to being looked at.