If you decide to use the T-nuts, here is what I learned. The T-nuts worked out well. However, on my first attempt, I covered the nuts directly with wood putty; and when I tightened down the joysticks, the nuts (slightly) pulled the putty down with the nuts.

Then I decided that a paper disc between the nuts and the putty would prevent them from being drawn down with the nuts. I found that the wax paper discs that those protective felt pads come on were perfect for the job. Now the putty sticks to the side of the holes and remains flush when tightening down my joysticks.
The control panel graphics would have probably covered the impressions but I made it flush anyway. Good luck.