Some suggestions and theories

[Jorge_Stolfi]

we have no reason to think he was a shipwrecked Indian writing in Malayalam

He was not Indian, he was born in Madagascar, and wrote in Malagasy (sorry for the typo).  He learned the Malayalam script from his mother, who was a Mappila from Kozhikode working as a You are not allowed to view links. Register or Login to view. at the Sakalava court.

the Northern Italian/Bohemian region where the parchment was fabricated (not to mention that he had a magic box full of Taccola, Kyeser and Duc de Berry manuscripts)

The parchment was manufactured wherever it was in the 1400.  It was bought in Bohemia by the Counts Rozemberk, lingered in their vellum discards box in for a century if two, until their guest John Dee bought it together with a dozen books from their library, before going back to England.  The box was not magical, just sturdy and waterproof.

And by a stroke of unimaginable luck, happened to come back with the book to the exact same Northern Italian/Bohemian region)

He never set foot in Central Europe.  After his rescuer took him to Spain, he enrolled again as a sailor aboard a Genoese merchant ship plying the Rome-Barcelona route.  In one of the stays in Rome he went sightseeing and lost his cherished Book of Dreams somewhere.  We now can tell that it was at or near Villa Torlonia -- because, about a hundred years later, the book was found under a closet by a Jesuit, who assumed it was the long-lost book mentioned in Marci's letter, which he then took out of the box of unbound Kircher's correspondence and attacked to the book, and filed the latter among the books absconded from the Collegio Romano in 1860. 

I know that this last part is hard to believe; but improbable things do happen sometimes.

All the best, --stolfi