In Unreal's Material Layer system, can I create a Material Layer that adjusts the saturation of the layers below?

BULL.

The landscape layers will never allow you to paint something that desaturates something else.

You can add, you can subtract.

That’s about it.

If you want to paint on top you can. That’s not altering the saturation levels.

Could you “use a layer paint that only affects all the layers after they are already combined?”
Maybe. Via custom layers.
If you expect to create a layer blend that does it for you you are SOL.

Go learn HLSL and write a custom node. Easier, more practical, and an actual solution since you can run desaturation or saturation algorytms you copy and paste with it.