Previous to this latest InfiniteScreen update you can actually run a renamed notepad.exe as EliteDangerous64.exe and vJoy will start outputting and useful in any game. The renamed notepad does not have to be in any game directory as IS is just checking process names (I assume). I run my renamed notepad from a temporary location.
What I have noticed is that within IS, I have to disable and then re-enable it for Elite Dangerous for it to pickup the renamed notepad.exe.
This might be all mute considering the updated IS which is supposed to allow vJoy output all the time. But I am hesitant to install it because I have things working fine as is for any game not just the ones Tobii wants to support.