I use one of default themes - Yaru-dark Gtk Theme. I installed it via flatpak as well. The application id is org.gtk.Gtk3theme.Yaru-dark. Some apps that I installed via flatpak follow it, but others do. I noticed, that apps that do not follow it use Gtk4 & libadwaita, so that might be the cause. Is there a way to make also the other apps use the system theme? I tried looking for org.gtk.Gtk4theme.Yaru-dark on flathub, but there is none.
$ flatpak remote-ls flathub | grep -i yaru-dark
Yaru-dark Gtk Theme org.gtk.Gtk3theme.Yaru-dark 3.22
For example baobab uses gtk4 and does not follow the system theme, while mypaint uses gtk3 and follows the system theme.

