Easy Fix, you need to trick Emulation Station into thinking something static that is always plugged in (a keyboard) is already configured. I edited my es_input.cfg file in ~/.emulatinostation and added a dummy keyboard. With a keyboard entry present in the configuration it will never ask you to configure a controller on reboot. That way i can reboot my Pi without having to worry about if my PS4 controller is connected via bluetooth or not.
<inputConfig type="keyboard" deviceName="Keyboard">
<input name="start" type="button" id="9" value="1"/>
</inputConfig>