I actually have a way to enter HBL & settings after launching an injected game but after that, only legit game will work until a reboot is done.Change before launching the game.
LayeredFS is unstable, I can not do more, anyway you can start in cfw mode and then in LayeredFS :/
1. Play injected game
2. close injected game
3. play legit game (it'll usually freeze at loading screen)
4. close legit game
5. you can now enter settings and or HBL, you can also launch any legit game and it'll be playable.
Edit: But still, we need to reboot just to play the switched injected game.