To add even more confusion, the common sense approach says to add any uncooked meats to the pizza last, so they have greatest exposure to the oven heat and are assured of being thoroughly cooked on the pizza, with that said, when making a Chicago style deep-dish pizza, the raw sausage goes on the bottom of the pizza, but it is thoroughly cooked due to the extraordinarily long baking time of these pizzas (about 50-minutes). The Chicago thin crust pizzas are also dressed differently with the cheese being put on last. Like Peter said, this results in a very soggy finished pizza as the melting cheese traps all that moisture under it, but again, this pizza is given a long baking time too, normally around 30-minutes. Most, if not all of the big box chains follow food safety practices of using nothing but pre-cooked meat toppings (due to the possibility of cross contamination, and the fact that they just need to be heated to above 160F to be safely served), and they like to keep the meat close to the top of the pizza to ensure thorough reheating/cooking.
Tom Lehmann/The Dough Doctor