Rio de Janeiro was Brazil's capital for centuries (even before it became an independent country), it only changed to Brasilia in the 1960s, well within living memory of many people, so that one is justifiable.
I personally don't see anything as "unjustifiable" - modern states can (and arguably should) be multipolar. Dedicating a city to administrative bureaucracy is not a terrible idea, in the same way as you'd separate salespeople offices from the factory floor. It's just a very modern concept.
I was just listing a few other famous "unintuitive" capitals. Another one would be Milano vs Roma, although the two are evenly matched on the cultural level.
