Non-transient utility or dialog windows (i.e. windows which have _NET_WM_WINDOW_TYPE set to _NET_WM_WINDOW_TYPE_DIALOG or _NET_WM_WINDOW_TYPE_UTILITY) cannot be iconified. If I understand it right this policy was introduced 6b385d5f53ce84fa05ba66955be0b3f5b7d794e4 and IMHO it should not be applied to non-transient dialog or utility windows since they can be the main window of an application. For an example see e.g. bug #7623, there are probably more applications which use a GtkDialog this way.
IMO it's correct from the window manager to disallow a dialog to be iconified, a dialog is not supposed to be present for the whole lifecycle of an application.
IMO those applications, that reuse the GtkDialog as their main window should call an extra function to change the window hint to normal instead of dialog.
Just my opinion.