How to square handwriting variation?

[Rafal]

Unfortunetely to decide which differences in letters are meaningful and which aren't you have to understand the text or have experience with people writing in different alphabet in different ways.

How do you know that all three letters in the top are A and three in the bottom are F?


It's your cultural background. It wouldn't be obvious to a Martian that they are the same letter.

With Voynich we neither understand it nor have other texts for comparison. So the cut-off point will be subjective and arbitrary.