Xfwm4 version 4.12.3 (revision 7fdcb53).
As in title there is feature "Raise window when clicking inside application window" is not working with GTK3 applications. For example gedit, gnome-disks is ignoring this feature.
I must say is not working with this feature disabled. Window must not activate like other GTK2 window for example.
No, it is not ignored by gtk3, it's simply makes absolutely no sense with client side decoration windows that gtk3 uses, precisely because the notion of "inside application" is unknown to the window manager as the decorations are entirely managed by the application.