While on 35, I had adwaita-dark set through gnome-tweaks.
Before upgrading to 36, reset that to light mode and uninstalled gnome-tweaks.
After upgrading to 36, I chose to enable dark mode.
I should expect programs like Thunderbird, firewall-config, AisleRiot to be in dark mode as well, right? They seem to have remained in light mode, and I don’t know what to do to make them follow the system theme.
Some apps are still GTK3 and wont use libadwaita. One option is to install the adw-gtk3 theme https://github.com/lassekongo83/adw-gtk3 and reinstall gnome-tweaks and set legacy-theme to adw-gtk ( dark or light ). There is also a flatpak theme to theme those too