I think the VM plants have a quite complex back-story and there is no easy and universal explanation for their 'weirdness'.
It is likely the artist(s) drew inspiration from several herbals regarding roots, leaves and plant-shape and some elements are quite faithfully copied, but I believe the flowers are their unique invention. Also some plants look more realistic than others and the quality varies greatly. I suspect that some plants were drawn after pressed specimens, others copied as a whole, some cobbled together from different sources and others fully invented by the artist. The 'stacking' of common building blocks is also a hint that the artist did not copy but drew some plants or at least plant elements from his imagination.
It is not unlikely that misinterpretations of both text and illustrations also played a role. Some elements of VM plants like the stem loops, flowers in flowers, flowers above flowers or root tables show a lack of botanical understanding. Even children know plants don't grow like that and even the most rudimentary herbal drawings do not show such behavior. See You are not allowed to view links.
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I know it appears to be an unpopular opinion but I still believe the artist/author had a certain lack of common-sense or difficulties correctly interpreting elements like perspective. He was also obsessed with stacking repetitive patterns and building blocks, both in imagery and the text.
As of why and what the overall purpose of the illustrations (if any) was, no idea. But to me it feels like the entire manuscript is an organic whole made up by a person with a certain mindset.