What does that mounting plate even do for you? It looks like either way you are going to have bolt heads showing through the top of the CP. Why didn't you use threaded inserts? Your CP looks like it is 3/4" thick, which is plenty of room to bottom mount. Or you can just have the bolt heads show. It looks fine honestly.
I was given advice that bottom mounting with that thing of wood could cause problems and crack the wood. Thus the S plate idea was brought up.
Are you suggesting I route an area large enough all the way close to board to fit the top of the joystick and forget the S plate?
Finally, I assumed I could screw the joystick into the wood shorter than the length to the top of the CP so the screws wouldn’t stick out.
Edit: without the extra 1/4” the S plate gave me.. so I need to be worried the screws won’t hold the joysticks steady?
When you say it looks fine, what are you suggesting I do?
Well, first of all, you are not supposed to route out material for the wings of that plate - only the middle piece. The wings are supposed to sit underneath the CP giving you the full depth to screw into. So you are already losing depth because you buried the entire plate. At this point you should forget about using that plate and see if there is a way to just recess the joystick plate. I can think of a couple of options:
1. Recess the joystick plate only (it looks thicker than the metal plate you tried so I assume you could remove a little more material. Maybe not. Then use round head carriage bolts (like on a DK) and bolt from underneath with the heads showing on top.
2. Recess the joystick plate so it is flush with the bottom. Use 4 very short screws to hold the joystick in place. I might add a few drops of super glue inside each screw hole or something just to be safe. Then use 2 wood strips on either side of the plate overlapping the bottom of the CP as straps so that the joystick cannot move or fall.
Also, since you aren't sure what you are doing I suggest making a mock-up before using the actual pieces. This problem could have been avoided using scraps of plywood I'm sure you have laying around. Get it right there and then copy what you did on the real thing.