The glyph [e] doesn’t usually occur at the start (or end) of a word. Depending on the transcription you use the number of tokens beginning [e] might be 150 or fewer. Given that other glyphs contain a stroke which looks identical to [e] it seems there is a strong possibility that the marginal occurrence of [e] at the start of words is due to a transcription error.
In a list of words beginning with [e] I found that in exactly half the cases the glyph was followed by another [e], meaning that the word begins [ee]. It would be easy to misread [ee] for [ch] were the “crossbar” of the [ch] to be very faint. In most, though not all, cases switching the initial [ee] for [ch] would result in a valid word.
I examined a number of words starting [ee] using the high quality scans provided by the Beinecke Library. These scans were not available when most the transcriptions in use today were made. In almost all cases there was evidence that [ch] was the correct reading.
Thus I would conclude that most words starting [ee] are in fact errors, and that the existence of [e] in the initial position is even rarer than believed. Of the words starting with only one [e], virtually all are hapax legomena, meaning that they exist in a single token. This suggests that they could be writing errors.
However, the word [ety] occurs 7 times in the text according to my list. A visual inspection shows that 6 of these are correct readings: the [e] is not another glyph and the word is likely to definitely separate from other words. Lacking contrary evidence I would consider [ety] a valid word and worthy of further analysis.
Yet we see that [ety] is not alone. Another 16 words start [et], and the total number of token starting [e] plus any gallows is over forty. Given that we have dismissed most words starting [ee] as misreadings, this [e] + gallows combination accounts for most of the words beginning with [e]. (Though a visual inspection shows that some of these are misreadings too.)
It is still a very small number, and [e] really must be considered as a glyph which doesn’t usually occur at the start of a word. But this small class of words might itself be valid, if rare. And I wonder if we are looking at a pattern or structure which isn’t strictly a rare part of the Voynich language, but rather belongs to another “language” which occurs infrequently as a “foreign” aspect, like borrowed words?
We can see other examples throughout the text involving all glyphs. Usages which seem different from the norm, common enough not to be writing mistakes but uncommon enough that they don’t feel normal.