I have built a motion platform and some hardware with dual encoders, buttons and switches, plus a throttle that I’d like to use. So despite my strap described above I would probably keep a controller on my lap when it’s supported, and grab it to operate virtual switches, buttons etc. I literally swear half of the time when I have to do it with the mouse, it’s so immersion-breaking and plain inconvenient - it hurts. Grabbing a controller and operating whatever is not in your hardware is much better just ergonomically.
As for the virtual yoke - nope, that’s very unrealistic and inconvenient. Virtual throttle kinda worked in X-Plane, but I had to turn my hand every time I adjusted it, to verify the grab. Hardware throttle is much more precise and intuitive. With joystick or a yoke - lack of resistance and inability to hold it just kills it. You can control the plane, but it’s so much worse than a real yoke - sort of similar to mouse instead of VR controllers for operating switches and buttons 
Hardware yoke, pedals are a must, and possibly a hardware throttle. And despite X-Plane encoded rotation in VR with feedback vibration clicks is amazingly cool, real dual encoders are much more precise and natural, so I think my VR Control Box would still be more convenient than controllers, for what it does.