The o's in VMS

[ololololo]

Now, however there is another point in this direction- manuscript may had been copied by different scribes, some of whom were not initiated to understand the subtle rules, but copied mechanically what they see and understand.

I assume that at least scribe A understood what he was writing.
Let's compare the writing of the letter a by scribe A (Botany) and B (Balneology):
   
The parts of a (e and i) are close together, and the spelling is quite stable.
Now let's take a look at the Scribe B:
   
I have underlined the special spellings in red. I can assume that scribe A may have parodied the Latin a to hide the encryption and deceive others. Scribe B was probably simply told how to write this letter, and he simply wrote it as best he could...