Why I think that the copyist(s)/scribe(s) did not fully understand the material

[Jorge_Stolfi]

I would not consider the first point to be obvious. It is possible that each scribe authored their own section. While unlikely in my opinion, it would make sense that the text for each thematic section was the work of one expert from start to finish.

Unlikely indeed.  

I wonder how many here have read Stanislaw Lem's tale of the guy who set out to find a Genius Of The First Kind? (That tale and his novel His Master's Voice should be mandatory reading for admission to this forum.)  

In the relevant time frame there must have been thousands of Geniuses Of The First Kind who invented a new script for some reason and used it to write a VMS-length book.  Societies with half a dozen members who did the same must have been much fewer, in the dozens or so at best.  So multiple Authors is a priori  far less likely than single Author.  Until we have evidence of the former (such as another document in the same script that is clearly by a different author), it is safer to bet on the latter.s

It is difficult, if not impossible, to cleanly separate the concepts of 'author', 'scribe', 'copyist' etc. in the context of medieval text production. Compilation, adaptation, re-arranging etc. were such key elements of the whole process that for a significant percentage of existing manuscripts we could not assign these roles even if we knew every detail about their creation.

Indeed, before copyright and photography, every copyist was an author, and every copy was a new book, to a smaller or greater extent...