A stock version of /opt/retropie/configs/all/retroarch.cfg should be fine.
Yours seems tweaked.

Try making these changes
xinput_player1_a = x
to
input_player1_a = x

Put a hash # at the start of these lines

input_player1_l2 =
input_player1_r2 =
input_player1_l3 =
input_player1_r2 =

Remove these lines (as your setup is pulling them from the auto config anyway)

input_enable_hotkey_btn = 8
input_exit_emulator_btn = 9
input_menu_toggle_btn = 5

Check this for multiple controllers: