I figured it out, at least for Nintendo.
I had been testing in Atari 2600, attempting to tweak both the retroarch.cfg file under /opt/configs/atari2600, in addition to the file under /opt/configs/all/retroarch-joypads/Microchip Technology Inc. Ultimate 2.cfg
I was doing some testing on Nintendo, and ended up doing the final modifications under the Microchip file referenced above.
Here are my settings, and "Enter" (19) is my new hotkey, and "6" (13) works to exit!
input_device = "Microchip Technology Inc. Ultimate 2"
input_driver = "udev"
input_l_btn = "14"
input_load_state_btn = "14"
input_start_btn = "12"
input_exit_emulator_btn = "13"
input_down_axis = "+1"
input_r_btn = "17"
input_save_state_btn = "17"
input_right_axis = "+0"
input_state_slot_increase_axis = "+0"
input_select_btn = "11"
input_left_axis = "-0"
input_state_slot_decrease_axis = "-0"
input_up_axis = "-1"
input_a_btn = "0"
input_b_btn = "1"
input_reset_btn = "1"
input_enable_hotkey_btn = "19"
Hope this helps someone.
Thank you for doing what you do.