First thought

[Jorge_Stolfi]

Note that Athanasius Kircher, ... one of the confirmed early owners of the VMS

Just to make good on my user title, let me point out that the only evidence we have for this claim is essentially Wilfrid's word.

The letters to Kircher by Marci, Baresch, and a couple other guys that supposedly mention the VMS do not describe it in sufficient detail to uniquely identify it as Beinecke MS 408.  They could have been talking about another book entirely. 

There is no solid evidence that Marci's letter was ever attached to Beinecke 408.

There is no note or stamp on Beinecke 408 itself that confirms that the book ever was owned by Rudolf, Baresch, Marci, or Kircher; or that it ever was in the Collegio Romano library, or was at any time in the possession of the Jesuits.  AFAIK there is no surviving catalog of Kircher's books or of the Collegio Romano holdings before ~1860.  It is not listed in any catalog or survey by them between their creation of the secret book stash in ~1860 and the supposed sale to Wilfrid in 1911-1912.

In fact, AFAIK there is no evidence that Kircher ever received the book from Marci, or that the book was even sent.  The cover letter that is kept at Beinecke was apparently written by Marci's secretary.  We do not know how Wilfrid obtained it; there is no mention of it, by the Jesuits or anyone else, before he announced its existence.  Thus that letter at Beinecke could well be a copy that the secretary made and archived for his own reference.  

Who knows, maybe the book was stolen or substituted, before it left Prague, by Marci's "friend" Raphael.  He believed that the book was a Roger Bacon original, in Bacon's fabled cipher, hence a treasure of incalculable value to an aspiring cryptographer like him.  It may be unlikely, but it does seem possible...

All the best, --stolfi

PS.  Ops, this post belongs in another thread.  Ho do I move it there?