Thepinkgamer, I think something like this was discussed a few different times. The problem is there is no universal button color scheme, so one would need to be picked which means colors (or markings, such as ABXY) are wrong for anything that doesn't use them in that order. It isn't as simple as changing things around in the emulator or game because some of us are used to the controls in specific games matching the default for that console, or because changing things around to match what is displayed is not optimal (or possible, as with N64 and other controllers that do things different).
Looking at my dummy main board it looks like there are LEDs near each of those buttons. It still may not be feasible due to the lengths that have been gone to so as to ensure equal lighting across the keymat (white under the mat, silicone designed to direct light to keytops, bossible reflective layer under paint on top of keymat). I am pretty sure there would be a lot of bleeding between individual buttons/LEDs. Also, since it wasn't planned it would mean more waiting for another revision of the board to get RGB LEDs added and everything tested again.
The best bet for something like Super Magnetic Neo is just to remember what color each button should be (look at the screen, not your hands
(looking at hands is something I still do far too often when typing)).
That clear case is really nice looking. I still think light bleeding out is not worth it, but it is a beauty. Now I am going to admire the pics for the next hour.