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

[N._N.]

Would the Scribe be the Author himself?  If you believe that there were multiple scribes, obviously all but one of them were not the Author.  But even if there was a single Scribe, I think that there is enough evidence that he was not the Author.  

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. The original post of this thread is an argument against this idea, but there are also scenarios in which an author-scribe does not fully understand what they are doing due to a lack of fluency in the cipher/language/whatever it is.

Additionally, to expand a bit on the C. Brewer quote mentioned by RobGea with what is my understanding on what is an author in this context: 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. With more than one person involved in the process, it obviously just gets more complicated.