Folio, Quire and Section Word Correlation

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I'm not sure I understand what exactly "the idea" is. Sorry, I can be quite slow when it comes to understanding various concepts

No worries and no reason to apologize, the idea is that a reusable encoding/enciphering mechanism is used to generate text as a way to obscure the underlying message. This mechanism can be setup to produce different output based on different settings. I say that different hands using different words is not an issue in this scheme.

Is it mainly about the correlation between folios and folios, between sections and sections or correlation between sections and folios (as in "this page correlates with balneology, etc")?

It kind of ends up being the same thing, the starting point was correlation between folios but as it turns out this confers correlation between sections and also quires.

To me this is not very obvious from the chart. Unless I'm reading it wrong, it correlates a bit with balneology and with a number of herbal pages, but doesn't correlate particularly well with the end section.

I think this is an issue of resolution, i.e the correlation between the bathing and recipe sections looks so strong that it blots out everything else. Essentially anything that isn't white is an above average correlation and is notable.

I think this is a cool idea (that plants and figures are generated according to some mechanistic process). It is reminiscent of various theories that "plants are not actually plants, but some schematic representation", but also explains why the plants look weird and many nymphs are in strange poses. Not sure if there is any relation to the study of correlations here.

You're right, it's not linked to the main body of the write-up, just something I threw in the speculation section.

As far as I know, this is a very popular idea and over the years a lot of systems and devices explaining how the words were produced have been proposed. Again, does the study of correlations play any particular role here?

Yes, the correlation suggests that the text adheres to the themes of the folio. If so, the mechanism that generates the text is not a random stream of generated text but text generated to a theme. That theme could be text related to that specific folio or section. The "vine" is a good example, it appears on 3 different folios and these 3 different folios have above average word correlation.

The question around generative text is usually positioned as "the manuscript is either pseudo-language or a cipher...", my point is that it can easily be both.

Thank you for the thoughtful and inquisitive reply!