@dojobaggins OK, so you might have had an older release where there was no 'Hotkey' button present in the input configuration dialog and Start + Select was automatically set. This is what you can do
configure you controller again in Emulationstation
when you get the Hotkey selection, just long press the A button to skip it, then save the configuration (press A).
there will be a prompt asking you if you want to use the Select button as a Hotkey, since you didn't assign a button to it. Choose yes here.
Now the Hotkey will be mapped to Select and you'll be able to use the same exit shortcut as before.