Distinguishing Characters

[MichelleL11]

...you can see in the plaintext that the same non-ciphered word is spelled different ways in the same line

So we can expect to find some words in the VM written in different ways, apart from abbreviations and ligatures?

Yes, it is well documented how spelling and grammar were very fluid at the time.  This is perhaps best studied in Latin, which had been essentially “reconstituted” from what classic texts were available and then “adapted” through cumulative interpretations and regional idiosyncrasies that were perpetuated from teacher to student.  

Some attempts to quantify these issues in medieval corpus have been made, see for example, Timo Korkiakangas, You are not allowed to view links. Register or Login to view., which l current only have access to the abstract.

But l’d like to emphasize that these issues are just an extra layer on top of the fundamental problem of the lack of grammatical “word patterns” in the Voynich text that preclude it, in my belief, from being a 1:1 substitution in any likely language.  If it is a cipher, some other text manipulations have occurred - likely more than one.  This is not my idea by any shape or form but something that becomes a necessity as you work with the text under the cipher theory.