Have we ruled out simple substitution unwisely?

[eggyk]

The core question is: "what is a single character".
We don't know the answer, but the Eva and Currier alphabets are on quite opposite sides of the spectrum.

I don't agree that that is the core question. In both cases a single interpretation for clusters of unclear strokes has been chosen. 

If I understand correctly, where Currier would use "N" and "M", EVA uses  "in" and "iin".

My (not fleshed out) idea acknowledges that in a case where plaintext Latin script "i, n, m" are simply a function of how many i strokes are present, allocating a single value may not be appropriate. 

To demonstrate what I mean, we can say:

Plaintext "i" = i   (or n   at word end)    
Plaintext "n" = ii   (or in   at word end)
Plaintext "m" = iii   (or iin   at word end)

Both currier and EVA would treat iin as the same every single time. But under these rules set out just above, we can't possibly say exactly what the plaintext was. 

In reality, it was either:
 "iii"  i + i + n   
 "in"   i + in 
 "ni"   ii + n 
 "m"  iin

The characters "minim" iiiiiiiiin ,  "immin" iiiiiiiiin , "nimnii" iiiiiiiiin all appear the same.

For the purposes of communicating about voynich, there isn't any issue. However, using the transliteration alphabets directly to calculate entropy ignores issues like this.