I’m using NixOS with GNOME, and I use Nautilus as File Manager.
I set Tokyo Night Dark GTK theme (tokyo-night-gtk package) and it works well on GNOME windows like GNOME Tweaks and I tested it also on Mate and Cinnamon DEs and this GTK theme works.
If you want Nautilus to use a dark color scheme, you can change the color-scheme key in org.gnome.desktop.interface GSettings schema to 'prefer-dark'.
If you do not care about “voiding the warranty”, then there is the option of using the third-party Gradience app to customize Adwaita, which modifies ~/.config/gtk-4.0/gtk.css. And there is also the GTK_THEME environment variable that can force change the theme but that is meant for debugging.
Mmm but on my Arch Linux I set the Nautilus GTK theme according to the set theme. My doubt is: is Nautilus GTK-4? If so, the only manner to manage it is to create a gtk-4.0/gtk.css file?
Yes, Nautilus is using GTK 4 but also libadwaita, so gtk-theme setting from org.gnome.desktop.interface GSettings schema will be ignored. Only the options mentioned above are available.
Yes, that is the debugging environment variable approach I mentioned. Just note that it is unsupported and if some app gets broken, you should report the issue to the theme developer, not the app developer.