Some letters aren't letters

[ReneZ]

There's really no problem at all with a sound that can only occur at the beginning of words, and the absence in labels is easily explained if q is a prefix that serves a grammatical function used in writing sentences that is not needed in labeling individual items.

This is basically what I am saying. It is not a rendition of a plaintext letter, but something different.
As a 'sound' I proposed a stop (e.g. glottal stop). It is, however, very frequent for that.

The labels obviously can't be verbosely encoded.  There's no way around this.

Here's an example of a herbal page with labels:

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The labels, consisting of three Greek letters, are in fact numbers.
The labels we see in the Voynich MS could be verbosely encoded numbers.