In your main retroarch.cfg

Remove these lines
input_enable_hotkey_btn = 6
input_exit_emulator_btn = 7

Just to be tidy, comment this out:
input_menu_toggle = f1
with
# input_menu_toggle = f1

Replace your entire fba retroarch.cfg file with

#include "/opt/retropie/configs/all/retroarch.cfg"
# All settings made here will override the global settings for the current emulator core
input_remapping_directory = /opt/retropie/configs/fba/
input_enable_hotkey_btn = "4"

This will make your left shoulder button the hotkey enable button.
So when you hold that and press Start it should exit the emulator.

You also had these settings which you may or may not want to add

custom_viewport_width = “823”
custom_viewport_height = “480”
custom_viewport_x = “15”
custom_viewport_y = “0”
video_refresh_rate = “50.000000”
video_fullscreen_x = “640”
video_fullscreen_y = “480”

I’d suggest leaving them out.