1.) The “script” is exceedingly regular, deliberate, and artfully embellished. The images are amateurish, even by medieval standards. Why the incongruity? If this were the work of a scholar, or even an eccentric member of the aristocracy, why would they allow the illustrations to be so poor? The limited colorization appears to be added after the outlines, apparently by a drunk guy painting with his toes. Why would they go to the trouble of writing and illustrating a codex comprised of hundreds of pages if the end result was so mediocre?

Hypothetical solution A: It could be the work of two people. For whatever reason, someone would do the illustrations, then pass them along to their friend in order for them to write descriptions around the images.
–> Problem: If the document is meant to be secretive, why involve collaborators? Both parties would have to possess equal knowledge of the subject matter, and work closely together to make this scenario work. Which leads me to…

Hypothetical solution B: The author(s) is young, possibly pubescent. Handwriting skills develop faster than artistic talent, and it’s natural for youngsters to be obsessively secretive (especially when drawing naked ladies and other such forbidden subject matter).
–> Problem: Aside from the fact that it’s difficult to imagine any young teen with an attention span long enough to complete a document like this, in circa 15th Century Europe, where would they get their hands on the materials? Even the spoiled child of a wealthy family would raise eyebrows buying vellum sheets in that day and age (which was becoming less popular than paper), and undoubtedly draw undesired attention to their project. This goes for adults with mental illness as well, as I’ve heard theorized. Thus…

Hypothetical solution C: The author is a crappy artist with nice handwriting, and genius-level code-writing skills. In order to preserve secrecy, the (adult) author forgoes artistry. Discretion is more important than technical aptitude; hence the elegant coded script paired with cryptic, childlike illustrations.
–> Problem: What kind of document this side of the Pentagon requires such an extreme level of secrecy? A Masonic diary? A treatise on the meaning of life, the existence of God, and the location of Area 51? Nope, a pseudo-scientific herbal/astronomical/medical/architectural thingamajig. Which brings me to another thing that bugs me:

2.) The fundamental problem I have with this being a composite of herbal/medical/astronomical knowledge is that those types of books are instructional; they’re meant to be read by other people! Writing the darn thing in undecipherable code defeats the whole purpose. Same goes for it being an allegory or fable. Those writings are only useful if they can be understood by other people.

Hypothetical solution A: The book contains such outrageous or profound information that it should never surface, lest the world be rent apart or lightening smite the reader.
–> Problem: The illustrations seem to indicate that the subject matter is not necessarily paranormal; They’re fanciful renditions of things found here on earth. There are researchers that have convincingly identified some of the plants, though theories abound regarding the “medical” drawings. The fact remains however, that these are not aliens, recognizable religious or political figures, or anything that could rock the proverbial boat. Even if the info really is that earth-shattering, wouldn’t the author eventually want SOMEONE to be able to understand it?

Hypothetical solution B: It’s actually never meant to be read, but more of a private diary or reference book.
–> Problem: Why would the author choose to use vellum over paper? Just to be posh? If it’s a private diary, not meant to be seen by anyone else, why go to the expense of making it on vellum? And if being fancy IS a concern, why the shoddy illustrations? It’s maddening.

My final theory: The author was some sort of eccentric, possibly with a mental illness, writing what they believe is an infinitely important magnum opus, but it actually means nothing.

Either that, or it’s an elaborate hoax meant to steal years off people’s lives as they obsess over this thing way into the wee hours of the night. In that at least, it’s a success!