Does anyone know what chemical process is used to stain decapped chips so that they are more visible?

A decapped chip will usually show metal very clearly, and when the metal is etched off the polysilicon and field oxide is usually pretty visible.

I'm wondering if you might mean something different from what I'm thinking of?

For example, here's a recent shot of the MOS 6522, very zoomable, most of the geometry is visible even with the metal layer intact.
http://ic.onidev.fr/map/6522.html

The only thing that's impossible to see on an unprocessed die is the depletion implants, but they are usually implicit in the shapes and the circuits that can be seen.

I think it depends on the chip. This is where I first heard the word "staining" in the context of chip decapping:

https://forums.nesdev.org/viewtopic.php?t=23983

Interesting - a rare case, I would think. In the linked page, Sean riddle says
> The 960-byte paramter ROM is at the top, but I think it must be implant ROM because I can't see any bits.

There are reference materials in and around
https://siliconpr0n.org/wiki/doku.php?id=delayer:dash