copy of an older, barely legible manuscript?

[Jorge_Stolfi]

The VMS was definitely written on paper first.

You will need to give your reasons for believing this.

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..  

the actual manuscript size is rather small. Only 9.3” by 6.4”. Since paper was more affordable and if there was a paper original would the paper pages not have been of a larger size? Perhaps the paper original, being an initial draft, would have included a lot of corrections, amendments? Perhaps, unlike VMS, there was no need to have to stuff quires 13 and 20 right up to the edges with small writing?

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.  

Unless the manuscript and its original version we're both written in the same weight of handwriting and on identical size sheets then line breaks would be different in the two versions.

And indeed the line breaks in the VMS paragraphs were almost certainly chosen by the Scribe, ignoring the line breaks in the Author's draft.  That is what scribes would normally do when transcribing running text from a draft or from another book.

There is plenty of evidence of that.  Like pages You are not allowed to view links. Register or Login to view. and f113r, where the Scribe changed the line width mid-paragraph because he found that the vellum was bad near the right margin.  

And yet the VMS line first words have a peculiar oddity

There are already some confirmed explanations for those line-start and line-end anomalies, including the side effects of the Scribe's natural line breaking algorithm and the subjectivity when transcribing word spaces.  Those may not be sufficient to explain the line start and end anomalies, but there may be other causes of the same general nature which we haven´t thought of yet -- that explain the anomalies, without implying that the line breaks were chosen by the Author and are somehow semantically significant.

All the best, --stolfi