The implication of this statement is that the federal government was in control of the process. My apologies if I misunderstood your representation here.
This still leaves my other points unaddressed. Contrary to your assertion, the Virginia v. West Virginia case didn’t address the ability of Congress to pick and choose who to accept as a legitimate government. It simply established that the Act of Congress allowing the admission of West Virginia into the Union at the request of Virginia implied that there was an agreement between the states about the borders to which Congress was giving assent, which fulfilled the requirements of the Constitution on the subject.