Yep, the challenge remains the placement of things around you in the real world. However, in VR, you could still set things up so that there is generally nothing around you and only the joystick and throttle controls would be of concern. If you can set your flight stick between your legs somehow, chances are it won't conflict with anything in the virtual cockpit. (I'm not sure how I could have avoided all that innuendo). You might have to move it a little to access the ejection lever in some aircrafts.
The throttle's position would be more challenging since you would have to place it in a way that it wouldn't block any of the buttons around it in the cockpit, or somewhere out of the way that would still be comfortable for you. Regardless of where you would place both controllers, with virtual hand tracking, you would still have to "disappear" them once movement on either controller is detected, just so you don't have floaty hands not matching with stick and throttle animations and position in the virtual cockpit.