ediff-prefer-iconified-control-frame is a variable defined in `ediff-wind.el'.
Its value is

If t, keep control panel iconified when help message is off.
This has effect only on a windowing system.
If t, hitting `?' to toggle control panel off iconifies it.

This is only useful in Emacs and only for certain kinds of window managers,
such as TWM and its derivatives, since the window manager must permit
keyboard input to go into icons. XEmacs completely ignores keyboard input
into icons, regardless of the window manager.

You can customize this variable.