When I took a botany course in college on the morphology of vascular plants, most of my drawings were far less realistic than some of these drawings. The fact the text weaves around the drawings seems to indicate a relationship (perhaps the description was added later.) The fact we don't recognize any of these plants either means the plants were some sort of hybrids or the author was an even worse artist than I was nearly 50 years ago.
I completely discount any theory that these are drawings of marine creatures which resemble plants - those kinds of things just weren't available to Europeans at the time, most coming from either very deep waters or from tropical reefs.
The fact the text seems like gibberish may be because it is gibberish. It is a documented fact there are so-called "idiot savants" who have a skill at one thing (art, for example) but who can't read or write or carry on a conversation. The neatness of the script in the 20 sample pages available through the link may be merely the attempt of some such idiot savant to replicate writing without having any other thought than the beauty of each character or symbol as the author committed them to paper.
Given the fact many monasteries of the period engaged in copying manuscripts on such materials with such colored inks, combined with the fact those same monasteries often acted as orphanages, taking in children rejected by society, it is not inconceivable such an idiot savant child came into a monastery and was allowed to play with writing and drawing materials. This is further bolstered by the fact the manuscript was originally received from monks and priests (the Society of Jesus - Jesuits.)
Ah well, just some idle speculation at 12:30 am on Saturday morning after a long week of speeches, storms, funerals, and lots of family and professional obligations.
Claus has often cited Occam's Razor: (It has to do with selecting the less complicated theory over a complex one, but really involves a lot more - I like to say it this way: "this theory will serve until we get enough data to move on to a more accurate one.")
In this case, my simple theory fits the facts so far in evidence and doesn't require positing alien intervention from outer space or alternate timelines and doesn't require 14th century Europeans to deep sea dive for Crinoids.