Okay, is there a reason that one can change allegiance while they have the capital of the realm within their duchy, but they can't secede? This seems to be an outdated holdover from the old-estate system. The new estate system mainly the Duke/Margrave separation mechanic seems to make this point somewhat antiquated.
Because you already control the capital of the realm. In a sense, you already control the realm.
Think of it this way: the Duke of Edimburgh can secede Scotland. The Duke of Cardiff can secede Wales. But the Duke of London can't secede England, that's already the main part of the realm. He can seize power in all of England through a rebellion, and then Scotland and Wales can secede if they don't like it.