“The South has contended only for the supremacy of the constitution, and the just administration of the laws made in pursuance to it.
“Virginia to the last made great efforts to save the union, and urged harmony and compromise.”
Robert E. Lee, Dec. 1866
The absence of one party to a legal requirement is not justification for that item being legally binding. For example, I cannot go to a bank and simply deem you to have cosigned the loan by virtue of your absence. ~ To assert that the assent of a State, even if it was in rebellion, is not really required when the Constitution explicitly demands it is to deny the Constitution's position of the highest law of the land.
To elaborate: Even if the Executive issued an Executive Order instructing the various Government Agencies to confiscate firearms, and the legislature were to pass [ordinary] legislation making all private firearm possession prohibited, and the Supreme Court were to declare these acts legitimate would not make them legitimate. Why?
Because the Second Amendment says "the right of the people to keep and bear arms shall not be infringed", and firearms are certainly arms, and such as above is certainly infringement.
The State of West Virginia was erected during a period of time in which there was no Virginia state goverment to assent or dissent the application of the loyal citizens of West Virginia for accession as a loyal state in the Union.
The absence of a State government to assent is precisely the point: a State government was required, by the Constitution, to assent... it did not. Therefore, for WV & VA to both be States, Secession must be valid: for either VA could not secede from the US and WV could not be a State, or VA could secede and WV could secede from that secession [and join/stay with the Union].