At the end it was quite simple following the hints outlined at
https://retropie.org.uk/docs/RetroArch/.
So I used
jstest to figure out main left/right fire buttons mapping of my two USB Joysticks and then simply swapped the values of
input_a_btn and
input_b_btn in the two corresponding retroarch joypad config files.
Now my C64 and Competition Pro Joysticks use left fire button for all games w/o the need to modify Amiberry custom controller settings.