The reproduction of roots as healing objects

[ololololo]

These are quite interesting assumptions, but the similarities to astrology seem rather forced.
The similarities with Balneology also seem ambiguous. Is the upper armadillo/sheep really a flower? Even taking into account the schematic nature, the author’s intent is not entirely clear.
I like your assumptions that the vessels in pharmaceuticals copy plants in appearance. But there is a simpler interpretation: the author drew the vessels as decorations and as certain markers to indicate the illustrations.
Regarding the Rosette's Island — the "cloud" might be something like pulp or seeds.

But it’s still a very interesting theory...