I have two laptops both with TW installed, on the first one every flatpak applications is in dark mode, gtk2/3 apps follow the settings I choose trough lxappearance and qt5/6 apps follows the settings I chosse troug qt5ct / qt6ct, gtk4 apps are just in dark mode.
On my second machine I’ve done literally the same things: set my preferred themes from lxappearance, qt5ct and qt6ct but no matter what I do, flatpak apps stays in default light mode. I’ve tried navigating the .config directory in both machine to see if there is any difference but I couldn’t find any.
Both machines are running a TW installation with “generic desktop (icewm)” and then using i3wm.
Hiya. Have you checked if you have theme installed in flatpak as well? Like do you see org.gtk.Gtk3theme.Adwaita-dark or org.gtk.Gtk3theme.Breeze in the output of flatpak list? GTK apps might ignore your theme until you allow them to read ~/.config/gtk-3.0 and ~/.config/gtk-4.0. You can enable that with those commands:
On my other machine I didn’t had to do nothing, no overrides and no variables. I simply set a theme with qt6ct/qt5ct and lxappareance and it’s respected trough all flatpaks.
That’s weird. I’m running Hyprland and those 2 steps were enough for me. Guess try comparing various system configs on both your machines to see if they have any differences.