Xfconf does not pick up the gtk-icon-sizes specified in theme's gtkrc. Querying xsettings/Gtk/IconSizes initially yields nothing, setting it to the value from the gtkrc makes everything work. This property should be picked up from the current theme and updated on theme change.
xfconf shouldn't, xfsettingsd should... I'll look into this, for 4.6.2
gtk-icon-sizes is deprecated since GTK+ 3.10, and is now ignored by GNOME apps. If Xfce is ported to GTK+ 3 this bug report should be marked invalid as we won't be able to implement was Mathias asked for.