Distinguishing Characters

[Mark Knowles]

(more difficult) the frequent occurrences of word repetitions. For b) it's hard to explain those if there is a one to one mapping between the plaintext and the ciphered form, right?

I think it helps to look at things through the lens of known historical 15th century ciphers. This is even useful if one only looks at cipher keys that are less similar than the Voynich. In that context repeated words could just be nulls. Alternatively, though less likely, there could be a specific rule for use in the instance of repeated words. Or this could be a long-form number representation e.g. "One One One" being 3 "Ten Ten Ten" being 30. I guess there are various possibilities though the idea of them being nulls fits best in the historical context that I am familiar with.