The pragmatic nature of the script

[davidjackson]

Secret" alphabets were not necessarily used to hide meaning. That concept seems to have arisen in the 14th century so is of course fully relevant for the Voynch MS.

However, apart from that, "unknown alphabets" were supposed to be a sign of learning, and knowledge.

Exactly, and I realise I left that out of my original post. This is what we see in the Arabic secret alphabets, they are essentially nonsense designed to impress.
European ones were often based on real alphabets, but it was obvious the writers didn't have much of a clue beyond the basic notions.
The Spanish also liked them - there was a roaring trade in nonsense charms sold for magical purposes, written in a PseudoArabic. 
And of course, the magic charms we see across Europe that are pseudo latín or Greek.