I only have a couple variants thusfar, and generating the rules file automatically makes that easier to swallow, but I very well might live to regret this. 
I do have such a rule, but it doesn’t work; it seems that an empty tile in an output region is simply ignored, not erased. There’s a DeleteTiles property for the entire map, but that seems intended for deleting the entire layer and then recreating it solely from rules.
I found a thread mentioning this, and it sounds like erasing tiles via automapping has never been possible. A property for the output layer that enabled erasing would certainly be handy.