URE shows in this list only capabilities available for deletion – capabilities which are not granted to any role, except ‘administrator’. 1st, revoke capability from all existing roles, then delete it via “Delete capabilities”.
WordPress stores capabilities in the roles only. ‘administrator’ role has all existing capabilities by default. URE looks if custom capability is used by other roles before decide if it could be deleted. Custom capability does not exist after deletion, until you will not add it back manually. When you add new custom capability it’s granted to the ‘administrator’ role automatically.