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

[Jorge_Stolfi]

This is very easy to explain by adjusting the argument a little. As you said elsewhere,

I meant, why was that situation specific to two whole arms and three whole stars -- instead of an half an arm here, half a leg there, a head over there, etc.

I don't know of any specific evidence that would point towards either of them

Neither theory has categorical evidence, like a glyph that looks unmistakably like a Chinese character or a 17th century C14 date for the dark ink.  However, both have lots of evidence that is hard to fit with the opposite theories -- which do not have any comparable evidence of their own.  What evidence is there that all the brown ink is original? Or that the language is not monosyllabic?

And neither theory requires assuming exceptional or unattested events, like a community of half a dozen anticlerical doctors who devised a new alphabet and a complicated encryption scheme to hide their secret knowledge of ... pansies? Or defective pens and inks that will switch unpredictably from nearly transparent tan to nearly black, at random, over a 200+ page book, and a Scribe who can't recognize the glyphs and body parts that he penned just a few moments before...

If true, neither of them allows for any easy progress in understanding the manuscript. ... Both MRT and the Chinese theory basically lead nowhere in practice.

Quite the opposite.

The MRT offers a quite plausible solution to hundreds of baffling puzzles about image and text details, like most hapax weirdos, words with os that should have been ys, and those crowns in the Zodiac. It would save Voynichologists from wasting time on trying to explain those details as intentional. It may make it possible to identify sources for the image elements that we can't recognize because they were mangled by the retracers.

The "Chinese" Origin theory does not immediately give a decipherment, but makes specific predictions about language statistics and word structure, and about the form a decipherment would take.  It says that each Voynichese word type is a syllable of a certain monosyllabic language, thus certain words should occur in patterns that would occur in a text of the expected nature (herbal, materia medica) in such a language.  And that the concepts represented in the Bio, Cosmo, and Zodiac sections would come from an East Asian culture, not from the "European" culture.  And so on...

All the best, --stolfi