It's less about food costs and more about the complexity and resultant labor costs, I think.

If that was the case then the first pepperoni slices would cost more, not the last ones. It's obviously market segmentation: somebody who really loves pepperoni will be willing to pay more per slice.

The cook time may go up since there is more mass.

Thick/dense components like dough/sauce/cheese I could see how the cook time increases more than linearly as the mass increases linearly. But with other toppings, there's no way the cook time goes up more from 48 to the hypothetical 96 than it does from 0 to 48.

It does affect the way it bakes and the texture, though, and can affect the way it browns. Vegetables have water. Meats have fat.