You would still need to set the target of the mass driver each time it moved as it cannot remember its last target since that could be in a different system. So, you're not going to be able to create fully automated mining operations, you're only reducing the number of clicks required each time a mining body is emptied.
Personally, I'd like to get rid of mass drivers completely and just rely on freighters and civilians. To be honest, I'm not really seeing the point in this module - just seems a way to make a portion of the game play itself, though I do understand that for some players, the ultimate endgame is to make a perfectly efficient self-contained empire that is 99% automated.