Why not positional variation?

[Scarecrow]

But who knows really. It could very well be a mixture of many ciphers, including substitution (assuming of course, the text is encoded plaintext and not gibberish)

While it may well be so that VMS is really enciphered real text, I feel we must keep in mind that the system to produce the VMS must have been also easy and fluid enough for them to produce anything with any reasonable effort. With the understanding and tech of in the 14th-15th centuries. 

Sometimes I feel many of the proposed systems do not take in account the persons doing the job. nor the general situation of technologies of that period. With some   exceptions of course, like Torsten's autocopy of wheel based systems, grilles to some extent, which would have been doable in the period and fluid enough to be able to produce something with reasonable effort and knowledge. Complexity is not human.