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

[Jorge_Stolfi]

the most important arguments are: ...  Traces of paint material are found on top of a later folio number. On the same spot where we know water washed over the whole area...

   

Indeed the spill that created that stain seems to have covered the folio number too.  

But the spill apparently was mopped up right away, because the green pigment that was washed away from the leaf was not deposited back onto the washed area, or along its edges (as seems to have happened in some other stains).  

So I think it is unlikely that enough of that pigment would have been deposited on top of the folio number to trick McCrone, Rene, and the conservator.

AFAIK there is no good evidence against the Late Painting theory; namely, evidence that the paints were applied in the early 1400s, by the original Author/Scribe or under their supervision.  Is there?

All the best, --stolfi

PS. Besides the paint, there are also overlaps between the ink of the drawing and both the green paint and the folio number.  It would be very useful if we had high-resolution (and in-focus!)  microscope images of those spots.