The Book Switch Theory

[ReneZ]

Just two initial points.

F4: In ~1911, Voynich acquired hundred of books from the Jesuits in Rome. Evidence: accounting records of the Jesuits.

Fact check: the best guess is 30-ish, as explained here: You are not allowed to view links. Register or Login to view.
There may have been some early prints as well, but I never looked into that. One or two of his catalogues might shed light on this.
It will not have been much, because it just increased the risk for the Jesuits, and Voynich would not have been able to make such a huge profit on them.

C2: Sinapius ever owned MS408.

In particular, the only evidence for C2 is the signature on f1r; but that is not good evidence, because there is no record of the signature having been seen by anyone before Voynich obtained MS408.

I have to disagree. An 'ex libris' is generally good evidence that a certain person owned a book.

I can see that this is an important point for your hypothesis that book A is not MS408, as it strongly links MS408 to Prague.

With respect to [C3] and [C4], I guess you will agree that they held one of the two.