reading through the forums and noted you mentioned this
"While a user could, in theory, fly using the Vive controller only, I don't think it would be a nice replacement for a joystick/yoke. You'd have to hold it in the air, your hand could get tired, movement would be less precise without back-pressure, etc. My plan is that the user would hold one Vive controller to manipulate radios, autopilot, etc, and use the other hand to control flight axis with a traditional joystick. That said, it will be flexible so that users can try things their own way too"
Just a heads up that I learnt to sim fly and still do the majority of my sim flying even today using a MS Sidewinder Freestyle Pro after buying up 3-4 on ebay years back for back ups too. Its one of those odd technologies that at the time in the 90's didn't catch on but then reappeared in the 00's and took off. Anyway you mention not using the motion controller for the axis but it might be worth looking into how the sensor button worked on the freestyle. When flying it is on and when I want to put the controller down or have the plane on auto pilot etc I just push the sensor button it turns the motion/gryo off and the pad uses the D-Pad for axis. Allowing me to put the controller down. After reading your comment I wondered if it might be worth you getting around any issues like you mention by having one of the controller buttons act as a simple on/off switch for the motion signals going to the software.
cheers,
Lewis