I think the chemistry involved is a bit more complicated than just deposits of soot and oxidation. E.g. metallic silver wouldn’t react with oxygen, but rather with sulphur compounds, giving initially a brown tint. Also the linseed oil carrier and varnish can change colour over time. During the oxidation of the linseed oil, radicals are formed that can react with a wide variety of other compounds. And light also plays a role with some pigments.
Added to that, there’s a wide range of possible pigments, of varying stability (and price!), and some techniques use layers of transparent colours (glazes), or mix pigments.
So, given the number of variables, I doubt you can get any reliable colour restoration just from a scan/photo of a painting. You could create an impression of what the original may have looked like when it was newly painted, but I think that’s the best you can hope for.
As for fees to get images, they are perhaps not copyright fees (hard to explain for a 16th century painting), but e.g. if the gallery is a private area, they can ask a fee to allow you access or to allow you to photograph anything.