Position a rack in the center of the oven and heat the oven to 450°F. Bring a pot of well-salted water to boil in a large pot with a pasta insert. Grease a 9x13-inch baking dish with 1 Tbs. olive oil.
Pour off 1 cup of juice from one of the cans of tomatoes and discard it. In a blender or food processor, purée both cans of tomatoes with their remaining juice and set aside.
Heat the remaining 2 Tbs. olive oil in a 6- to 8-qt. Dutch oven or heavy-based pot over medium-high heat. When the oil is shimmering, about 1 minute, add the onions and 1/4 tsp. of the salt and cook, stirring occasionally, until nicely browned, 5 to 10 minutes. Push the onions to the side of the Dutch oven with a wooden spoon and add the garlic. Cook until it just starts to sizzle and becomes fragrant, about 10 seconds.
Add the puréed tomatoes and cream (be careful; it will splatter), plus the remaining 1 tsp. salt. Bring to a boil over medium-high heat, reduce to a gentle simmer, and cook for 10 minutes, stirring occasionally, so that the sauce thickens slightly. Add the parsley and the red pepper flakes, and cook until the flavors are melded, about 5 minutes more. Taste for salt and pepper and remove from the heat.
Meanwhile, when the salted water comes to a boil, cook the rigatoni until it’s al dente, about 10 minutes. Drain the pasta by lifting out the insert and leaving the water in the pot. Add the pasta to the sauce. Return the water to a boil (with the pasta insert in the pot) and cook the cauliflower until barely tender, about 2 minutes. Drain and add it to the sauce.
Add 1-1/2 cups of the shredded Fontina to the pasta mixture and toss well. Transfer to the prepared baking dish and spread evenly. Top the pasta with the remaining 1 cup Fontina and then the Parmigiano-Reggiano.
Bake uncovered until the cheese is golden brown, about 15 minutes. Let the pasta rest for 10 minutes before serving.
Photo: Scott Phillips