Have we ruled out simple substitution unwisely?

[ReneZ]

But hypothetically speaking, what if each of those transliteration alphabets share some underlying aspect that causes the issue? These results would then due to a systematic error instead of the VMS itself. It would be good to rule this out as far as possible. 

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.