Right, the thing with joypads with more than 7 functions (up, down, left, right, 3 x fire) is that they weren't simply one wire to one switch, thus requiring a more advanced protocol. The SNES and CD32 both fall into this category, and you can be sure their protocols are different. This would mean not only rewiring the small contacts inside, but also transferring over the communications chips from one to the other. A lot more difficult than changing a C64 joystick to a Spectrum one

The reason a Megadrive one will (partially) work on a CD32 is that they both retain the old Atari compatibility for the D-pad and one or two of the buttons, and only the remaining buttons need encoding to fit on the remaining pins.