Fixed in trunk r2352. Mixxx now looks for "Custom.kbd.cfg" in the same directory as your "mixxx.cfg" file. (This depends on your OS.) If that file is present, it will override the standard one. (You can verify this in mixxx.log and/or the console output in the first few lines. It will say "Found custom keyboard preset.")
Fixed in trunk r2352. Mixxx now looks for "Custom.kbd.cfg" in the same directory as your "mixxx.cfg" file. (This depends on your OS.) If that file is present, it will override the standard one. (You can verify this in mixxx.log and/or the console output in the first few lines. It will say "Found custom keyboard preset.")