Why not positional variation?

[pfeaster]

One can formally describe rewrite rules to take Voynichese closer to a hypothetical "underlying structure" which the writing system doesn't always represent directly. E.g. Emma did this with her hypothesis of You are not allowed to view links. Register or Login to view..
Emma's post tries to make sense of [o] and [a/y] as corresponding to two entities with very similar roles in word-structure. Though there may be other explanations, an obvious parallel is phonetics and how vowels are largely interchangeable.

Another way of analyzing this would be to observe that [o], [a], and [y] all begin as [e], but are then each closed off by a different concluding stroke.  That is, if we compare word pairs such as [daiin] and [dy], or [qokaiin] and [qoky], which Emma found appearing in remarkably consistent ratios, it may not be that [a] as a whole is alternating with [y] as a whole, but that the "roots" of these words are actually [de] and [qoke].  The word [daiin] could then be decomposed into [de], plus [\\\\] (four minims), plus the upward curve that forms an [n] with the final minim.  Or, if [n] is just a terminal variant of a minim, we could further reduce the structure to [de] + [\\\\].  But either way, the heuristic advantage of treating [a] and [y] as ligatures in this context would be that the structure Emma describes would arguably be represented directly in writing.