All of the issues here with custom controls are fixed in the latest Amiberry development branch. We have also introduced some level of retroarch controller integration.
It's not a retroarch emulator, but the controls setup stuff is nice enough for us to have used the setup conventions, rather than try to create something new. Maybe in future I will ad support for FS-UAE controller files also, as this was a big inspiration for the approach.
If we are lucky, we will try to have it pushed to the master branch by xmas.
