My readings of the plant labels

[Koen G]

Actually yes, but this may be generalized without detriment to my argumentation. Say, the botanical section "introduces" plants into the book (for whatever purpose), and the pharma section "makes use" of plants (whatever use).

There is no one to one correspondence.  The botanical section makes the commercial value of some plants easy to remember, the small plant section teaches the vocabulary. Some plants are in both sections, some aren't. 

As a sidenote, that means that the local names can be conveyed through the same script as the non-local names. Generally, no problem - you could e.g. transmit Russian with English alphabet (although not very neatly).

All local names are phonetic transcriptions. All the reader was interested in was what the word sounded like. He didn't want to learn a dozen scripts. Indeed, some areas wouldn't have had written language at the time. The reason Voynichese script was invented at some point may have to do with this as well, but that is too speculative at this time.

First, this still leaves unexplained why the supposed local names for some plants are found in the botanical section

I haven't spent a lot of time studying this, but some possible explanations should be clear from the partial overlap between the plants. Also, maybe the local name is mentioned in some parts because it happened to be needed there, while on others they just talked about the use. 

About the paragraphs in the small plant section, I haven't studied those in detail yet. I would hypothesize that the main language is the one familiar to the reader. If these paragraphs list possible variations for the local plant names though, they may mostly be composed of often similar foreign words, with only some Greek or Latin words to give structure.

The star name being the same as a plant name can be explained through homonyms. Indic for juice is /ros/, while in Dutch this word means horse or red haired. In other Indic languages the word for juice is /ras/, which is the Dutch word for race or an archaic word for fast. Especially in these short words, but at times also in longer ones, such coincidence can be expected. 

Besides, even if we stay within the same language, one word can have very different meanings, so I don't see why this should be a problem.