The app puts themes in ~/.themes and ~/.local/share/themes, which makes them come up twice in GNOME Tweak Tool.
I find that GTK2 and GTK3 themes (and GNOME-Shell themes) work fine from ~/.themes, it's only Metacity/Mutter themes that don't show up in GNOME-Tweak-Tool unless they're in ~/.local/share/themes.
The app puts themes in ~/.themes and ~/.local/share/themes, which makes them come up twice in GNOME Tweak Tool.
I find that GTK2 and GTK3 themes (and GNOME-Shell themes) work fine from ~/.themes, it's only Metacity/Mutter themes that don't show up in GNOME-Tweak-Tool unless they're in ~/.local/share/themes.