While that's a logical chain of deduction, it ignores some very important facts.
First of all, it has always been possible (though very rare) for a capital to go rogue or defect to another realm all on its own.
Second, it has always been possible (though difficult) for another realm to run a successful takeover of your capital.
In both of these situations, the region remains the realm's capital, even though it is not in their control, and they must manually move the capital to another region.
While I don't recall specifically whether we considered this situation when we were making the changes that decoupled cities from duchies, that was many years ago now, and we have seen situations like this come up multiple times since then. We are very comfortable with having the realm's capital outside the realm when this occurs. We have even added code to ensure that when that happens, people returning to the capital (such as when released from prison) are not sent to enemy lands, but rather are told that their realm no longer controls its capital, and they must choose a new realm to "return" to, as if they were rogues.
