Either that, or https://xkcd.com/593/
People have always been people, we've always been creative and intelligent, and I really think the best explanation is that this is just an odd creative work. We'll never know the exact details.
It's also known that the text makes no sense as an encipherment known in the 17th century of any known natural language. Statistical analysis of features suggests it's not random gibberish... but also distinguish it from natural language. It's also prone to a high degree of repetition or near-repetition (think phrases like "burgle bugle bugie", with one-letter changes between successive words).
Personally, I think it's gibberish that was constructed to have some degree of plausibility for a would-be cryptanalyst. Or maybe even something as prosaically simple as calligraphy practice, given the unnaturally repetitive nature of a lot of the text.
But that's a very ahistorical theory, isn't it? The manuscript was written hundreds of years before cryptanalysts were invented. For its author to anticipate that would have required an impossible degree of foresight. Rather, whatever features give it cryptographically interesting properties must have been motivated by something other than a desire to confuse/intrigue cryptanalysts, with that just being a coincidental side-effect.
Presumably the concept of a coded message followed pretty rapidly after the invention of the written message.
In other words, the pictures are the original thing and main content. I would guess they're not about bothanical stuff, but instead use names of bothanicals and other alchemical ideas from the era it was written.
My guess is based on the idea that plant names and alchemical ideas last a long ass time. They're perfect for encoding something meant to not be changed by common text-altering techniques (adding punctuation or accents to non-puncuated or non-accented languages, deriving letter-casing from non-cased letters and so on).
The theories various people have had fall into three categories: it's in an unknown language, it's enciphered, or it's meaningless gibberish.
Which in my opinion makes the old Marco Polo delegate theories the most probable, but all through the lenses of European culture.
The theory isn't popular because it doesn't reveal anything but once you look at the book it seems likely. The notably thing is the symbols don't have the variation of a language - they are less complex and more locally repetitive.