Comment 2 for bug 1788547

I think the issue is that Yaru redefines the system gnome-shell theme, and none of the themes in /usr/share/themes have gnome-shell themes in them, so all themes inherit the new Yaru gnome-shell theme.

A workaround is to enable user themes (eg see https://askubuntu.com/questions/545741/why-is-shell-theme-disabled-in-gnome-tweak-tool) and to install themes that supply matching gtk-2/3 and gnome-shell themes. Then you can select a matching gnome-shell theme using gnome-tweak-tool, so if you're using a dark application theme you can choose a matching dark gnome-shell theme.

Example themes are Obscure-Orange and Numix-gnome-shell.

An interesting side note is that although Yaru-dark from gnome-look.org provides a dark gtk-2/3 theme, its gnome-shell theme is the same as Yaru-light.