One potential problem is that classical polyalphabetic polyphonic ciphers would lead to quite a few repeated characters in the ciphertext, as seen in the examples in the article I linked. In Voynichese, with the exception of I/E clusters, repeated characters are quite rare.
But I'm not sure we are talking about the same thing. Could you give a short example of the type of encoding that you have in mind?
But I'm not sure we are talking about the same thing. Could you give a short example of the type of encoding that you have in mind?