copy of an older, barely legible manuscript?

[Pointless..]

I already gave one: it would be insane for anyone to write anything directly from one's head onto vellum, considering how expensive vellum was, and how hard it is to correct errors.

Another evidence for the Scribe copying from a draft is the You are not allowed to view links. Register or Login to view..  
Yes!  And that is another good argument for the book having started as a paper draft.  Because writing those small letters with fine pen on those small pages was a task that required non-trivial care and skill, hence was better left to a "professional" Scribe.  

There is also the possibility that the manuscript was written and encoded using a plaintext family book as the source. I have contemplated the hypothesis that the VMS represents a ciphered version of a pre-existing, plaintext family or guild archive. If a sudden turn in the legal or ecclesiastical climate rendered their traditional plaintext books and archives dangerous, encryption would have been a necessary protective measure to safeguard sensitive intellectual property from the prying eyes of inquisitorial or state authorities.
If the scribes were part of the family or the guild, they material was possibly already familiar to them so encoding should have been easier.

So yes, they would never had committed to vellum without a source text ready.