> I think things like the Banach-Tarski theorem are the other side of that coin: they're showing some of the places where the formalisation we're starting with isn't a great fit for some things we might hope to use it for.
I don't follow. You can view the Intermediate Value Theorem as something that motivates the definition of "continuous function", so that once you have the definition it had better conform to the theorem, sure.
But the Banach-Tarski theorem isn't like that. It's just a cool result of some other things that work well. It's not motivating anything or being motivated by anything.