Following both the instructions here (which work fine on 4.0) - Contents/dark-theme.md at master · Qubes-Community/Contents · GitHub (setting a dark theme in Appearance Manager)
And also adding settings.ini to .config/gtk-3.0 && .config/gtk-4.0 with gtk-application-prefer-dark-theme=1 (which also works in 4.0 fine) - MOST things in dom0 go dark with these steps, the taskbar, most of the app windows, nautilus/thunar windows, etc.
Most things but Qube Manager. Anyone know why this might be? Does manager require a special separate setting somewhere? Does it not use GTK?