> So, what is the new, more common meaning? That exception to the rule somehow strengthens the rule?
Yes. And the fact this meaning is meaningless, or at least a very dishonest tactic, doesn't really change the fact it's now the most common meaning.
Pragmatically, the lesson here is that "the exception that proves the rule" is a bad phrase to use unless you're deliberately trying to confuse or derail the discussion.
> It's not meaningless, it's precisely how it was/is used in law
I mean the current common meaning is meaningless; to wit: "Exceptions to the rule I just propounded make the rule stronger, as opposed to disproving it."
> Two other idiomatic expressions that have similar confused usage are "proof is in the pudding" and "begs the question"
The first is misquoted ("The proof of the pudding is in the eating" is immediately obvious) and the second is a horrible translation which would have gotten a failing grade in any school which taught Latin and which should be forgotten.