I'd point out that you're assuming this is a
natural script.
That implies that the script has "evolved" alongside the underlying language to cover all eventualities.
Let us assume for a moment it's not, as Bax has postulated - it could be a script devised to encode an existing language for a specific purpose. In which case, the phonomes would be limited to those the creators assumed existed.
A real life example - 16th century aljamised Spanish (Castillian written using the Arabic script by the conquered Moors of early christian Spain).
The Spanish was turned into a partial abjad - the first writers didn't cover vowels, but then discovered you couldn't reinterpret the Spanish without some vital ones. So they continued to drop most vowels except for important ones, which were indicated by modified consonants or diacritics. O and U shared the same diacritic.
You ended up with 28 Arabic characters (plus four vowel diacritics) encoding all the sounds of Spanish. But, and this is interesting, many of the sounds were encoded using different letters
depending upon their positional function in spoken Spanish.
Which is exactly what Bax is arguing. I'm not supporting his theory here, simply pointing out a real life example.
Here's the list, pinched off a You are not allowed to view links.
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[spoiler]
Letra árabe
Transcripción
Consonantes
ا
Ø, h
ب
b, v, p
ت
t
ث
t
ج
ch, j, g
ح
h
خ
ch
د
d
ذ
d
ر
r
ز
z
س
s, ç
ش
x, s
ص
s
ض
d
ط
t
ظ
d
ع
h, Ø
غ
g
ف
f
ق
q, qu, c, k
ك
q, qu, c, k
ل
l
م
m
ن
n
ه
h
و
gu, gü, hu
ي
y
Vocales
َ
a
ا َ
e
ِ
i
ُ
u, o
Digram "ch" (which was important enough to warrant its own letter in the old Spanish alphabet) is encoded twice, once as a stand-alone sound and once grouped together with /ch/,/j/,/g/. This, I assume, is simply because of its function in spoken Spanish - it can be pronounced three ways, depending on how it's forming the word.
We see the same effect with other sounds such as /d/, /s/ which are assigned to different letters.
Taking it the other way, we see the sounds
/gu/, /gü/, /hu/ all lumped together to one Arabic letter.
This doesn't prove anything with Voynichese, of course. But it is an example of how people developed new scripts for existing languages.