Sorry I got confused there.
Can you tell me how you disabled 360 pad support in Steam?
I did disable 360 support in big picture mode, same as you have in that picture above (because enabling breaks the navi inputs somehow), but it still makes the navi act as a 360 controller in SteamVR.
For me that is ok, I just either use SteamVR home to launch games, or directly from the desktop. And in-game the navi is usually always working fine.
Hope that makes sense.