There is a special glass box mesh that needs a special geometry, the d100 one. When the inner depth is smaller or larger than the outer, than the outer front and back faces go over the faces of the inner box, or through the inner box, thus we could close them without any graphic problems.
But if we made the d100 mesh in the way we did the d25 one (section 4.6), than the front faces of the inner and outer box fall together, SL may have a problem to decide what one to display. The same happens for the back side. To avoid those problems, we have to make holes in the outer front and back sides, even if this causes more complex mesh geometry.