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I think you are correct, but that point was disregarded at the time and since.

The North stated before the war that secession was illegal; the South disagreed. When it was convenient to carve West Virginia out of Virginia, for that purpose the North changed its mind.

After the war, the North (Congress) said that the South had left the Union and had to be readmitted, while the South said they never legally left. The main reason for this is if the Southern States had come back into Congress immediately after the war, then the Republicans would have lost control of the Congress. Naturally, they didn't want to lose control after winning the war, so they acted like politicians: power over a legal principle they had previously held.

I'm not personally criticizing the likes of Thaddeus Stevens and Ben Wade on this issue: I am sure that if I was in their shoes, I would have made the same choice. Successful politicians need to change tack if they want to keep winning, because the electorate are fickle.

Yes, but if the war was fought under the assumption that Virginia didn't have the right to secede in the first place, then the Constitution still applied to it, right?

Article IV, Section 3:
New States may be admitted by the Congress into this Union; but no new State shall be formed or erected within the Jurisdiction of any other State; nor any State be formed by the Junction of two or more States, or Parts of States, without the Consent of the Legislatures of the States concerned as well as of the Congress.
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So, with the consent of Congress and of the Virginia legislature, West Virginia could be formed from within Virginia.

Perhaps Congress conveniently ignored the requirement to get the consent of the rest of VA, but, after the war, there was no motivation to force WV to re-join the rest of Virginia, which would have necessitated their consent to the new junction, especially with the politically expedient reasons the other poster explained.

And, after all, if the North lost the war, at least they would have part of what was formerly Virginia.

I wouldn't know if Texas could exempt themselves from a provision of the US Constitution, since statehood requires ratifying the Constitution, but it appears that Texas (or CA) could split into several states with the consent of Congress and of the Texas (or respective state) legislature.