I'll try to answer that. When a (clear) gem is faceted, in general
you are aiming for a maximum return of light, maximum "sparkle". In
other words, all the light that enters through the top should be
totally reflected back out of the stone by the pavilion facets.
The facet angles which give this total internal reflection depend
upon the index of refraction of the particular gem material. Total
internal reflection also means that you can see into, but not
through, the stone when you look down at it from the top.
If the pavilion facet angles are cut too shallow, you can see
through the stone, and this area is then the "window".
I recently cut an emerald (emerald cut, in a kind of stubby, coffin
shape) for a friend which unfortunately had a pit at the very bottom
of the pavilion. So I needed to lower the pavilion facets angles in
order to cut this away. The result was a noticeable, albeit small,
cross-shaped window at the bottom of the stone.
Cheers, Hans Durstling Moncton, Canada