A nice theory except that you wouldn't be able to paint under any of the support structures built into the case plastics, so a uniform colour would be impossible. If that floats your boat, that's great, but it wouldn't be a good solution for mass production.
I think you misunderstand what I wrote: the mass production would be "transparent cases" (as well as normal non-transparent cases), NO "painted transparent cases". Painting transparent case would be self-made by end user if he wants to color it. ED would sell a transparent case, and if you want to paint it, it would be your task.
Except holes for screws, I think you can paint the transparent case elements without problem as fine spry painting doesn't add important thickness. For example paint thickness on a new vehicle have an average of 120 microns (divided in different layers).
In this thread we can see pics of case (in particular the top part with holes for keys/etc:
https://pyra-handheld.com/boards/attachments/dsc03637-jpg.32656/ ). I don't see the problem for painting it, other than having to cover holes for screws and top surface with adhesive so that painting doesn't stain it (you want to paint inner surface, not outside surface).
Even, if you want, or if it is necessary, you can cover with tape small parts (for example borders) that support a plastic piece against other plastic piece, so that you doesn't paint those small surfaces.
Of course,
I could be wrong. And of course if you add a lot of layers or you use thick paint, you can end with too much thickness to parts fit properly.