Ideal mounting for Sanwa sticks is 3/8" below the surface.
Dont route out anything, 1/4" ply + 1/8" plexi is perfect.
If you are worried about flexing, put in a stiffener bar or additional supports, or both like I did on my first stick:
8 Supports instead of the more traditional 4 corner supports:

Glued bar to center of the panel for additional stiffness:
