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

[ReneZ]

But several people who have looked at the folio number with  a microscope (not just Rene and others at the workshoop, but, now I see, even the McCrone guys)  all agree that the paint is over the ink.

Do you have any exact quotes on this? 

For the observations by Rene and others at the Folgers workshop, there is You are not allowed to view links. Register or Login to view.. 

For McCrone's claim, there is You are not allowed to view links. Register or Login to view. by Rene.  There is another one somewhere, but I cannot find it...

All the best, --stolfi

If the second quote refers to this:

This statement was reported in Viennese newspapers after the press briefing in 2012.

However, this is not in the McCrone report and it is also not what was analysed by McCrone.

I should clarify:

this did not refer to the order of the application of anything, just that it was done soon after the parchment was created.
While the latter is normally the case, this was NOT determined forensically.