Sorry for a late reply.
To be honest, I don't care much about OpenLiero, as the goal now is to port LieroLibre (which has a remappable "dig" button). I believe the menu items are loaded from the DOS EXE, yes, which means you need to hardcode the dig action. Adding a config file for the button assignment sounds like a pain, since if it's not reachable from the game, people will not use it or even know about it's existence. There is no easy solution I'm affraid.