Why and how the text could be Bavarian

[ololololo]

No hard algorithm to encode / decode.

Think of one-time pad. The essence of this cipher is as simple as possible — the key must match the length of the message and be used only once. But anyone who doesn’t have the key will never be able to decipher it.
The VMS cipher may well be difficult for us, but for the author it could have been easy, or at least worthwhile. He also had an advantage over us — he knew more about it than we did...

This super-complex cypher theory would have been too awkward for the writer.

Here, I’ll say that I don’t know whether @JoJo_Jost is discussing the entire manuscript, Currier A, or Currier B. For Currier A, for example, such a cipher would be quite suitable, since the pages of Herbal A usually contain rather short text excerpts. The author didn’t bother with them much.

The argument about complexity only works when it makes the algorithm impossible or overly cumbersome. Don’t forget that you’re looking at a book that has defied decipherment for 600 years. Is it really worth relying on a substitution?