Just to sum this whole thing up for me:
I finally set the pcb into Gamepad-Mode using the serial Monitor in the Arduino IDE. Then I configured the controls in Emulation Station. After that things went wrong. lr-mame2003 didn´t recognize any buttons, whereas Emulation Stations UI did work flawlessly. I tried several things, setting the driver to udev, sdl, sdl2 and whatnot, editing ArduinoLLCArduinoLeonardo.cfg as stated in the original post, trying this in retropie 3.8 and 4.1 and so on.
I didn´t get it to work, so I switched back to keyboard mode. After that I did try to map the keys of Defender and MK using mames tab-menu (did connect an extra keyboard for that) and not the RGUI of retroarch. This did work perfectly, I finally have working and playable configurations for all my critical games using more than two buttons :-). Conclusion for me: retroarchs per game remappings don´t seem to work, mames built-in menu is key to success. One last question: does anyone know where the keymappings I generate with the tab-menu are stored? I searched around the /opt folder but couldn´t find any clues.
Happy Retro Gaming ....