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

[Jorge_Stolfi]

That's not the case with VMS. As @Rafal already wrote, it seems unfinished. Part of the “message” it is supposed to convey is lost without color.

First, what information is the green paint conveying, exactly?  The unpainted outline already "says" that the area is a pond. 

Second, it is indeed possible that the ink outline we see today is incomplete.  The green paint would have washed away any ink that it was painted over.  Wherever there is water flowing into the pond, one can still see traces of the flow line continuing well into the painted area: but very faint, so that we would not see them if it wasn't for the parts that were not painted over.  

This is the case on this same page: at both ends of the "mug handle" channel on the left margin of the pond, and at the top, where the two feeding streams pour into it.   

So maybe there were other details inked in the big area at bottom, that were painted over and thus washed away.

All the best, --stolfi