Heat oven to 350 degrees Fahrenheit. Coat bottom and sides of a 13x9x2-inch glass baking dish with nonstick vegetable-oil cooking spray.
Cook rotelli pasta in a large pot of lightly salted boiling water following the package directions. Drain the pasta well.
Meanwhile, mix together the shredded cheddar, mozzarella, and Jarlsberg® cheeses and the grated Parmesan cheese in a large bowl.
Over medium heat, melt the butter in the pot in which the pasta was cooked. Whisk the flour into the melted butter until well blended; continue to cook, whisking constantly, for 2 minutes to eliminate flour taste. Whisk in 1 cup of the milk until well blended. Gradually whisk in the remaining milk, 1 cup at a time, whisking after each addition until well blended. Stir in the salt, nutmeg, and ground red pepper. Bring the mixture to simmering; cook, whisking constantly, until thickened and smooth, about 2 minutes. Remove saucepan from heat. Stir in 2 cups of the cheese mixture, whisking until the sauce is very smooth.
Add the cooked pasta to the cheese sauce in the pot; toss together until well blended.
Sprinkle 1/2 cup of the remaining cheese mixture evenly over the bottom of the prepared baking dish. Spoon half of the pasta mixture into the baking dish, spreading evenly. Sprinkle 1 cup of the cheese mixture over the pasta. Spoon the remaining pasta mixture over the cheese mixture. Sprinkle the remaining cheese mixture over the top of pasta. Arrange sliced tomatoes over top of casserole.
Bake the macaroni and cheese in the preheated 350 degree oven for 45 minutes or until the top of the macaroni is lightly golden. Let dish stand for at least 10 minutes before serving.