Yes you can use per game config for every game you like its so simple
Right click on any game you like to use per game config > Edit > Emulator >Check Use Custom command-Line Parematers
then type --fullscreen --cfgpath="GameConfigs\YOUR GAME NAME"
press ok
now run the game , you will see there will be error because you didnt setup the new config its ok close it , go to your emulator folder then enter inis folder and copy all the ".ini" files then back to your emulator folder and enter GameConfigs folder > your game folder and past all inis files here
now go to Launchbox and start the game , setup the game as how you like after you done just close it , all changes will be just for this game.
just remember to copy inis for new games config so you dont need to remap your controller every time etc