Please set gsettings key for selected gtk theme
When choosing a gtk theme in appearance please set
gsettings set org.gnome.desktop.interface gtk-theme NNN to the gtk theme name (and potentially also set
gsettings set org.gnome.desktop.wm.preferences theme NNN for the window manager theme).
Without this being set flatpak is unable to automatically determine which gtk theme packages should be installed.
Furthermore, apparently this setting is now set by other DEs such as KDE and according to gtk/gnome developers is correct to set for gtk themes.