No, it's not specific to the RetroArch version, overrides don't save the hotkey configuration, it's saved only when saving the whole configuration.
You can try to add an extra configuration line in /opt/retropie/configs/gba/retroarch.cfg with


where X is the button input code for L2 - you can find it from your gamepad autoconfiguration file in /opt/retropie/configs/all/retroarch-joypads/<gamepad.cfg>.