After years (hours) of looking for an answer, unable to find a working one, I'm going to ask you.
How do I change the color of this (or any other than gnome app) to match the dark theme? I find it highly annoying, and the solution that everybody suggests (gnome shell theme) simply won't work.
I've enabled custom shell themes, but not a single shell theme that I would even consider using have changed the color of these windows.
This is what my tweak-tool looks like:
Under window (or any other than shell theme), there's nothing else but adwaita and high contrast.