Some suggestions and theories

[ololololo]

I advise us to get more insight into this topic, for you do not know much yet. In fact, such conclusions are as simple as possible (for obvious), but hollow and empty. 

Based on the pictures alone, I make the assumption that it is some work of science

Naturally. We can even identify the theme - it's most likely medicine in general, not just medicinal herbs.

manuscript is not "cyphered", it is written in its own language.

Voynichese itself is not a full-fledged language. The theory of an artificial language also falls away - it is too redundant. However, it can still be a modified language (German, Occitan, Bavarian, Chinese, etc.).

Otherwise you would need to decypher it every time you need it and it wouldn't practical (especially if the "cypher" doesn't have a simple solution).

If you know what you're writing about, even an encrypted text will make sense to you, because you'll remember what it says.
If you know how it's encrypted and use it frequently, you'll start to remember what you need over time.

Why own language: my grandma speaks Polish whenever she doesn't wants others to listen to her phone conversations. Here the reason might be similar: if you are a secret society, then with a language known only to the initiated, you can hold conversations anywhere without eavesdrop.

You might as well use a local, little-known language, or a language whose speakers are not in your usual environment. I don't know of any examples where secret societies created their own language, ciphers were always preferred.

the manuscript was dictated by someone (for ex. professor to a student), thus the one who draw them didn't saw the actual plants, he only had the word descriptions of them.

Some of the plants are probably redrawn, or at least real, which means that the author had the opportunity to learn what a particular plant looks like. However, I am unable to explain why the plants are modified or unclear.

Thus it's reasonable to assume that the plant pages of the manuscript contain words for leaves, root, flower etc.

There are no such patterns. And there is no place for them there - we are presented with a drawing of a plant, and with good eyesight, we should not have any problems perceiving how it looks. For a healer, the external characteristics of a plant are not as important as its functionality and healing properties.

with the help of a Botanical Expert, we can pinpoint (a biome) the location where the manuscript was written

The place of writing is somewhere in the Alps (of course, they are talking about Northern Italy, but the author could have been somewhere else). 
The plants were examined. She didn't find anything extraordinary.

I had a similar opinion at the very beginning of my own research. You should delve deeper into the information about the Voynich manuscript. You can read this forum, websites voynich.nu and ciphermysteries.com, and other sources.