Why and how the text could be Bavarian

[JoJo_Jost]

Do I understand correctly that you suggest not simply Bavarian but some "obfuscated" Bavarian - with null words, repeated words, phonetic spelling, tricks like Pig Latin ( You are not allowed to view links. Register or Login to view. ) and so on?

Yes, that is correct, but I believe that Latin phrases only appear in the first lines, precisely to mislead the solvers.

If the author's plaintext was bavarian-austrian slang that was shortened, which only could be understood by a select few people (if anyone at all), why go through the extra steps of:

1) changing the plaintext letters to a ciphertext
2) inserting red herring latin markers in only the first lines in order to make it harder to understand

How would another reader (presumably a student, friend, or colleague) read the manuscript? How would they know which words are null words if they are by definition placed at random?

I think he was afraid. Certain topics were dangerous enough in the early years of the 15th century to land you in prison or worse.
A shorten Bavarian dialect alone would have been too easy to decipher – especially since there are similarities between the different dialects.
The Latin markers would be a perfect deception, especially for scholars, church people, judges, and others.

You can only read it under the following conditions, and I can reveal that much:
1. You have to know the cipher code.
2. You have to know the dialect.
3. You have to know what the text is about.

In principle, zero words can already be recognised in the text if you know how they are constructed (e.g. the same word with a letter shift). But I think they are a little more complex to recognise, although I don't have an idea for that yet.

All this sounds very interesting. I think you are on a good track and I look forward to your second part.

Thanks, so far it's just another theory, but it could explain some of the strange things  of the VMS.