Preheat the oven to 450 degrees F.
Bring a large pot of water to a boil and cook the rotini al dente. Drain and spray with olive oil cooking spray, making sure the noodles are coated well. Set aside.
In a large saute pan over medium-high heat, cook the bacon until crispy. Remove to a paper towel-lined plate. Remove all but 1 tablespoon of the bacon drippings and add the butter. Add the onions, garlic and nutmeg. Season the vegetables with salt and pepper and saute until the onions wilt and become translucent, about 4 minutes. Reduce the heat to medium-low and sprinkle in the flour, stirring to coat the onions and garlic. Continue to cook until you have a blond roux, about 5 minutes. Whisk in the milk until you have a thick enough sauce that it coats the back of a spoon. Crumble the bacon and add half to the sauce. Mix in the Cheddar and mozzarella. Turn the heat to low. Add the pasta to the cheese sauce and stir to coat. Cover and keep warm.
In a small bowl, add the breadcrumbs, Parmesan, chives and olive oil. Add the rest of the crumbled bacon and add it to the bowl, stirring well to combine.
Spray the pizza dough with the olive oil spray and place into the oven for 7 minutes. Remove from the oven and set down. Spread the macaroni and cheese on the pizza, being careful to leave a 1-inch border. Sprinkle with the breadcrumb mixture on the macaroni and cheese and bake in the oven for 10 minutes. Remove from the oven and let stand for 10 minutes to set the macaroni and cheese.