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

[Jorge_Stolfi]

"given that there is now strong evidence that many of the bifolios and even quires were scrambled several times over the manuscript’s history and yet nearly all the paint transfers appear to be between pages in their current order, it seems that a great deal of the Voynich Manuscript’s paint was added later on in its life"

ciphermysteries --> "Voynich colour inference, a sure path to madness…"
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That is a good argument... However, plaing the devil's advocate for once, could it be that the paint transfers happened much after the painting, when the relevant pages were exposed to humidity?

(There is a big water stain on You are not allowed to view links. Register or Login to view. that spans the whole page, for instance.)

Tempera paints usually are not waterproof.  I would expect the binder to be gum arabic or other organic glue, which would soften if exposed to water for more than a few seconds...

All the best, --jorge