Why not positional variation?

[Koen G]

One problem we may be facing is that we have not yet been able to establish a concrete, viable alternative to the extremes.

Simple(ish) substitution, as espoused by most theorists, is suitable for the historical context but not for the system of Voynichese. And nonsense generation (Timm, Rugg...) can be shown to suit the system, but is historically unattested at this scale. To my feeling, a wide chasm looms between these extremes, and we don't know very well what's in there. For example, we could try assuming positional variation to convert Voynichese to something like Roman numerals, but then what? As long as there is nothing to aim for, we cannot test any hypotheses.