Making them round is so inefficient for the machines. Make 'em long -- that way you merely need to pass dough through a conveyor. Then, use the money you saved on the simpler machinery to do an advertizing campaign to change the public's perception of what shape a pizza should be.

The boxes are already square. Two long rectangle pizzas in a box. As a bonus, it's easy to pack two DIFFERENT pizzas with different toppings into a mixed box, for group orders. And variety.