The Unlimited Useful Life Of US Stamp

QRs are different. If someone was counterfeiting wouldn't they want them to be the same?

The QR code should be unique, different on each stamp, like a serial number or a concert ticket, such that when the stamp is scanned at the post office it gets marked in the system as cancelled and cannot be used again.
I wonder if the counterfeiters found a way to hack that part as well, to get past the security check at the post office so that the stamps scan successfully, or whether they all get rejected and returned to sender as invalid postage.

The counterfeiters don't care about the mail getting through. Their interest is in the money generated by sales and the problems it causes to the mail system.

I couldn't find any mention of invaliding pre-Civil War stamps in the Scott catalog stamp listings. (Maybe it's buried in the introduction material.) From what I can tell, Scott #62B and higher (issues of mid-1861 onward) remain valid, but earlier ones were devalued so the Confederate states post offices stamp inventory of U.S. issues would be useless.

That's correct.
Same with the postal stationary of the era - i.e. Nesbitts demonetized.

Yes, it is somewhat hidden. The Scott Specialized catalog has considerable text following #72 inclding the following snippet: