The consequence of set_transient_for() failing with a TypeError is that the Object Chooser of an activity is displayed over other activities and also over the Journal.
It fails because the Gtk.Window is passed from toolkit to the shell through DBUS as an integer, the XID of the X11Window (GdkWindow). It is sent in toolkit's ObjectChooser and catched in shell's JournalActivityDBusService . So at the other side we have a GdkWindow.
So I've found that calling the method with the same name in the Gdk.Window fixes the issue. There is no error in the log, and the Object Chooser acts as a dialog, attached to the activity Window.
http://developer.gnome.org/gdk/stable/gdk-Windows.html#gdk-window-set-transient-for
Patch attached.