I propose we add country selector to payment type editing screen and checkbox, that will indicate, that payment types is intended to use selected below countries. During checkout only payment types not linked to country (from order) or payment types, that match order's country will be displayed to user.
What is unclear to is what to do in case, when primary payment type won't match order's billing country. Then what payment type should be set to order.
There also were similar request in forums: