I also needed to install a dark theme to flatpak with
flatpak install flathub org.gtk.Gtk3theme.Adwaita-dark
to get the application ID... Then the following command to apply the theme to the application ID... For example with LibreOffice
flatpak override --user --env=GTK_THEME=Adwaita-dark org.libreoffice.LibreOffice
That command worked great in Hera, but it seems to be hit or miss in Odin. It will hold for a while... even occasionally after a reboot, but ultimately it seems to lose the setting and default back to the flatpaks "light" setting.
GTK_THEME=Adwaita-dark as an Environment Variable in Flatseal seems to yeild the same results. Works for a while but in Odin, it seems to disappear. In Hera it appears permanent.