The makers of RUBI insist that no two rules of a rule set can ever apply to the same subexpression.
That's draconic, and verifying that would be, erm, "interesting".

I'm not sure whether that's worth it, but they do have a point if they say it's the only way to be sure that no rule is applied in an unexpected way, which is what I get is the main point behind most of the problems you mentioned. Also, it would force rule writers to investigate into which rule's turf they are breaking, and reconsider whether their addition is actually an improvement over what's already there.

I can't say what's the best approach, I'm just collecting potentially relevant arguments here and hope somebody has enough breadth of vision to properly weigh them all.

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