There is an appreciable difference between the time it takes to close
the last epiphany window and the time it takes to close any other
epiphany window. It seems as though Epiphany is doing housekeeping
before withdrawing the last window. Perhaps it's even leaving that to
the housekeeper?

As far as I can tell, epiphany would never need to present an alert or
otherwise interact with the user after a window has been closed.
It should therefore withdraw windows as soon as the "delete-event"
signal is received, and only then proceed to the invisible details
of normal program termination.

I grepped through epiphany sources for "delete-event", but could not
find it; perhaps it's hidden behind some other wizardry.

For a Gtk+-only program, doing what I describe should be as simple as:

 g_signal_connect (app_window, "delete-event",
                   G_CALLBACK (gtk_widget_hide), NULL);


The delay before the last window is withdrawn is often so great that
Metacity's unresponsive app alert appears.