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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