Some suggestions and theories

[Rafal]

I am just a passerby with some mild curiosity about the manuscript

Hi!
Many of your observations are quite rational but unfortunately it doesn't help us much 

Some stuff is impossible like Freemasons who didn't exist yet in the 1400s but these are details.

Another things seem quite logical like "Thus it's reasonable to assume that the plant pages of the manuscript contain words for leaves, root, flower etc.". However they just don't work in this case   Don't you think people tried it before?

Voynich Manuscript is bizarre. Don't listen to people saying that it is standard medieval manuscript, just written in unknown script. It is weird. 
The images are weird but you have to get some experience and  see a lot of other manuscripts to notice that
And the text is weird too. You just don't have good candidates for "leaf", "root" and "flower" words. You also don't have good candidates for the most common words like "and", "so", "with" etc.

If you ever get interested in Voynich Manuscript more, you will start to discover these weird things.