There are several reasons for it. It is much more convenient to transport square boxes. The stack of square boxes is much more stable, nothing falls and does not turn over. Getting a pizza out of a square box is just easier. After all, otherwise, its sides would fit snugly against the sides of the box. Free space allows you to deftly wield both a spatula and your hands. Due to the fact that there is a small air gap remaining in the box, the pizza stays warm and fresh longer.