It’s more a solution on a system level, say on externally maintained apps that insist on having the input key in the “down” position (snes B) as the accept button that ignore any input changes you make in Gameshell OS that this pertains to. But if you’re just doing simple emulation, it probably doesn’t affect you, and it wouldn’t be a solution. Each to their own 
On a side note, re retroarch key config messing up, as long as you’re only changing the settings on a per core basis, you can’t possibly mess up anything, as long as you keep the global settings intact. See the link below.