Good question. It sure is confusing. I have three instances of ED installed. I started on Steam. Then I got the Rift and installed it in there. Then I thought I might have performance problems so downloaded it again ("Commander" edition from FD) to run outside. Right, when I fire up standalone ED it starts the Oculus s/w.
You can toggle the mode, 2D or 3D, inside the ED game itself. Go to Main-Menu>Options>Graphics>VR. Turn it off and click Apply, and it immediately goes into 2D. Change it to HMD and you get immediately get 3D. You don't have to reinstall or even quit the game.
The only wrinkle is that if it starts up in 3D, you have to put the Rift on to enable changing it to 2D.