I suppose it depends on a few factors.One: Are you comfortable in your level of skill in whatever form of customizing you are intending to do?
In this case, you're talking about doing some painting. I, myself, would not feel comfortable with trying to do that. The closest I have come is some work with a silver Sharpie, but typically I limit my customizing to things like incorporating third-party add-ons. (New accessories, replacement parts, or Reprolabels.)Two: What are your intentions towards this figure?
Are you a collector concerned with the value or potential future resellability of your figure? Or do you collect more for your own enjoyment, but you are greatly concerned with keeping your figures as "mint" as possible? Then customizing is likely not for you.
But are you the sort of person who collects purely for personal reasons, and is not afraid to do things that potentially decrease a figure's public value in the pursuit of making the figure better fit what you want in your collection? Then have fun!
I might have a few examples in my collection, I suppose. The best one would be Orion Pax. So we have an E-Hobby exclusive figure, not something usually thought of as extremely common in the States. In this case, it is just a recolor of G1 Kup:(Image from TFWiki)
Not a bad looking figure... but really not Kup. (Also, that photo is not to scale! That would be a huge Dion figure!)
But, slap on a custom head and some Reprolabels, and you get this:
A much better looking Orion Pax in my opinion. And something I like a lot better as a part of my collection then the stock figure. But, objectively, a devalued figure. Missing its original head. A bunch of random, non-original stickers slapped on it. Far from mint. Thus, potentially a wrecked figure in the view of some other collectors.
So, in the end, all of us can express our opinions on the merits or dangers of customizing rare figures. But in the end, what you have to ask is what you
want out of your