How could we tell if VMS is original work or a product of copy from another MS? What evidence and indications we could expect to see to confirm either case?
Producing something like VMS was not so small feat. The producers of the VMS had to do some planning like deciding the subjects, plan format - layouts and illustrations, gathering resources and materials, recruiting required skills, etc. The calf skin parchment used in VMS was dated to 15th century, and while it is not great quality, as Rene has written, it was still carefully prepared. Did the producers of the VMS make it by themselves or did they buy it? If they did it by themselves, what would that indicate?
The encryption/encoding system. Did they create a novel new way or was there available other systems which they could have borrowed, and maybe integrated and changed for their needs? The VMS encryption systems seems to be made fit-for-purpose but creating such a system just for one MS seems quite implausible to me. Maybe VMS used as PoC as they wanted to use the system for other things also but for some reason their plans got cancelled.
Creating such a writing system is not any small thing in the 15th century, without much of theoretical base, knowledge and examples available, not something you do just for one thing.
And after the encryption method was done, they needed to create correspondent glyphs and rules/conventions to support the encryption/encoding system, aka. the writing system. And they had to write it down somewhere to train the involved people, as we have indications that there have been more than 4 writers/contributors doing the VMS, and also to evolve the system from Currer A to Currer B. So, the whole writing system, rules and methods, had to be written down somewhere. Also, JKP has quite extensively shown that most of, if not all, the VMS glyphs bear a resemblance to the then common Latin/Greek letters. One or five glyphs could be considered a coincidence, this many it is unlikely and is more a reasoned choice.
The question is, why did they adopted the Latin letters as the base for the glyph-set design, when they possibly could have freely designed a completely new set of glyphs, adding another level of protection to the VMS? Why did they still wanted to have mix of original and conventional glyphs?
In any case, creating such a writing system takes time and resources to make, and requires possibly not so commonly available knowledge and skills. Who at 15th century could have had the possibility fund such an undertaking and for what reasons? And who had the knowledge, skills and resources to design, define, plan, organize and execute such a thing? A family? A Monastery? A trade union? Ruling parties?
Illustrations. If VMS was a copy of a MS with the illustrations, then they just needed to copy them to the VMS. Possibly the different dimensions and the new writing system of VMS may have posed some technical difficulties transferring the illustrations as is from the plaintext MS. There are indications like Anton's line breaks and alignment, Philip Neal's findings that lines have been written in different order, and Anton's idea of multipass to suggest that the illustrations gave some headache to the producers. Maybe they had to change the writing system rules later to better accommodate the text within the drawings. In any case, at least some of the persons in the team had to be able to read the original text.
But if the original MS did not contain illustrations, why they wanted them in the VMS? Maybe as mnemonics, maybe as tags to connecting related folios together? Or maybe just to confound anyone from the true meaning of the text, images that to not relate in any way to the text but for any casual reader or church investigator seem to be normal herbarium etc.
While there are plenty of unique vords in the VMS (8486), 6014 appearing just once, there seems to be no names/nouns, not for plants or other, or there is some kind of context rule where a vord would be interpreted as a proper name.
And of course, there is the question of why encrypt/encode the text? If it was a copy of a plain text MS, maybe it was considered too dangerous in the place they were and decided to encrypt it. If the MS was already encrypted, then go ahead. But then we are looking at an encryption system that is older, maybe from the 14th (or even 13th) century. But does for example the glyph-set design support this possibility? If the work was commissioned, the producers naturally had to comply with the order, but why anyone come to order to have both encryption/encoding AND new glyph-set designed just for this? Or did the party commissioning the work know already, that those people had this system already in place and chose to use them because of it? There is not much convincing evidence that the scribes were very proficient with the writing system, at least not in the beginning, so it would go against the idea that the system was already developed, unless they used new scribes for the job. But then they had to expand the knowledge of their system, potentially exposing it. They wouldn't have done that, would they, if the texts done with the system were .. potentially dangerous, or tremendous secrets.
All of this, of course, if the VMS was meant to be readable. I have seen so far many reasonings why VMS would not be readable or a hoax, none of them so far convincing. But then again, nothing in VMS is truly convincing. I believe it has a meaning, and not just an intellectual exercise, which is left to the readers.