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

[Jorge_Stolfi]

Recent XRF elemental analysis on ff. 1r and 1v did not find any evidence that the pigments were later

Element signatures in inks and paints should have remained mostly the same until the 1700s, when synthetic pigments started to replace natural minerals.

I wonder what was the very dark blue pigment used on the flowers of f3v, f4v. f17r, and a few other pages.  It seems different from the lighter blue pigment used on f16v, f69v, etc., which I can believe was azurite. Did McCrone analyze it?

except for the Marci annotations, which are zinc-gall and therefore confirmed as post-medieval.

Zinc was a common impurity in green vitriol, hence in iron-gall ink. But do you have a reference to that "zinc-gall" ink?

The suggestion that the pigments must be later because of the offsets makes no sense to me. It's just the opposite. The offsets suggest that the manuscript has been in its current state for centuries.

Again, ofsetting of tempera paints can happen any time after they are applied, if humidity is high enough.  

All the best, --jorge