What's the evidence that the colors were added later?

[Jorge_Stolfi]

Whatever the deliberate use of colors means (not forgetting yellow and red), it is not simply decoration but, as I said, a pictorial narrative. It should therefore be seen as a visual commentary on the text. It is virtually impossible that the colored illustrations are nothing more than a kind of interchangeable ornamentation.

Well,I take issue with the "deliberate" here.  Everything about the paint layer, from the "instrument" used to the general disregard for the outlines, tells me that the Painter did not know or care about the meaning of the illustrations, and saw his task as being just decorative.  In particular, he seems to have picked colors at random, apart from some loose constraints like 

• "leaves are often green"
  
• "roots are usually brown or ocher"
  
• "sun rays should be yellow"
  
• "nymph's hair is light yellow"
  
• "star cores are yellow (or, in the Starred section, alternating yellow and red)"
  
• "rain and running water is usually blue"
  
• "still water is green or blue"
  
• "sky is usually blue"
  

He was somewhat careful with outlines on the first few herbal pages, but later he would often do a crude job.  On the Bio and Zodiac sections he was quite careless about that, and often painted over inked details (like the tail and paws of the "otter" on f79v.

You are not allowed to view links. Register or Login to view. is my idea of what the nymphs of You are not allowed to view links. Register or Login to view. actually looked like when the original Scribe was done with them.

The interpretation “a pond is just a pond” clearly falls short here.

I agree that we cannot assume "a pond is just a pond" in this section.  Either the organs are metaphors for ponds, or the ponds are metaphors for organs, or both are metaphors for something else.   On this question, I am still as baffled as everyone else.

But we should not expect that the colors will help us solve the riddle.  I believe they are only noise, that adds to the confusion...

All the best, --stolfi