I may have stated this explanation before, but----
I live in Chicago. A lot of the pizza joints are either owned or worked by Hispanics. From what I understand with these great people, food is either cooked or not. What is this "well-done"? I have learned the phrase "bien cosido" for my burritos for this reason. Now understand that any good pizza place in Chicago will top a pizza with raw pork if sausage is ordered (and that's my regular). So, if I have a worker who is baking my pizza and to him "cooked" means cheese melted and crust firm, than chances are the sausage is close to raw, considering that it is under cheese and amid sauce. Or it may even be that the owner is worried about complaints of the pie being overcooked, so they pull it from the oven early. In either case, I'd like to have my pork fully cooked and my crust solid and crispy, if possible. Sometimes at some places, even well-well-done is not followed as ordered. I've told a place that I want it cooked long enough to have the cheese turn brown. So what they did is undercook my pizza(again) and then throw it under a broiler until my cheese was dark brown. I knew this by the fact that the dough was soft and barely cooked. It's a matter of safety, in a weird way, and also about flavor. Let the sausage(or other meat ingredient) blend with everything.My cheese pizzas are never well done though.
Another simpler reason is that growing up in the early 70's all South side pizza places cooked their pies to a medium to dark brown cheese bubbles on top. Those were always the best spots on the pie (and the corners too!). It's a matter of what one is used to.From north side to south side, from city to city, and coast to coast.