The thermodynamics of ovens can be quite complicated and I am willing to go into more detail on the subject if you'd like, but I believe that the simple answer to your question is that air is an insulator with poor heat transfer characteristics and low heat capacity (the ability to retain heat) relative to the pizza stone and the other internal components of a home oven, so even though the temperature of the air in the oven and the temperature of the preheated stone can be the same, the pizza will bake faster from the heat of the preheated stone (through heat conduction and heat radiation) than through the heated air surrounding the pizza, whether the stone is at the top oven rack position or elsewhere. Unfortunately, home ovens are designed for multi-functional applications, i.e., to bake all kinds of things and not only pizzas. Hence, they have more space between the top and bottom than commercial pizza ovens (e.g., deck ovens) where there is less air above the pizza and more heat available from radiation from the sides and top of the ovens, as well as by conduction from the hearth suface itself, which collectively allow the top of the pizza to bake in a more balanced way with the crust.
Because of the inherent shortcomings of home ovens for baking pizzas, that is why many of our members play around with stone positioning, using more than one stone (to get better heat capacity and "foreshorten" the oven), and using the broiler element. And some have convection ovens that circulate heated air (by convection) around a baking pizza to get a better balance between the baking of the bottom and top of the pizza.
Even within a pizza itself, the principles of thermodynamics are at work. When the unbaked pizza is placed on a preheated stone, the crust expands and, because it is filled with gases (air and carbon dioxide), as it expands it behaves as an insulator between itself and the pizza stone. The pizza sauce has high heat capacity and low conductivity, so it will act as a barrier between the crust and the cheese. The cheese, being a high fat product, has high heat capacity (i.e., it melts easily). Consequently, the size of the pizza and the number and types of toppings will also play a major role in getting the right balance between the top and bottom baking. Of course, it goes without saying that the dough for the pizza has to be properly made. Otherwise, the top and bottom can bake up differently and not be done at the same time.