Flatseal, Iplan, AdwSteamGtk, and any other libadwaita app I install through Flatpak use a broken version of the legacy Adwaita theme:
I have deleted the gtk-3.0 and gtk-4.0 folders in the past in order to allow them to be managed by home manager, but I have repopulated them with Gradience (Adwaita Dark preset) and Home Manager. Still, there is something wrong.
My current config is here: mars-monkey/nix
GTK3 apps and native GTK4 apps respect my adw-gtk3-dark theme.
You can press Ctrl-Shift-i to open GTK inspector. Then you can look at what theme is picked up.
You will need to make sure the theme is packaged for Flatpak. That appears to be the case for adw-gtk3-dark.
But how did you even force it to use a different theme? Theming libadwaita apps is not really supported. Did you override the debug environment variable?
I did override the debug environment variable in my Home Manager config, everything works fine with it disabled. Thank you so much!