I don't get it. Which GUI do you mean, EmulationStation, RetroArch or what? And why should it be toggle able? If it's for EmulationStation, why not split the roms into the different systems?
I think the good way id to create 2 core option files and launch the game with correct option file depending u want to launch in jap 60hz or use 60 hz or pal 50 hz.
Is possible in gamelist to set the lauching command specifically for each game?