Cook pasta according to the package directions, omitting salt and fat; drain. Lightly coat pasta with cooking spray.
Heat a Dutch oven over medium-high heat. Coat pan with cooking spray. Add onion and carrot, and sauté 4 minutes. Add garlic; sauté 1 minute. Add ground beef; cook 5 minutes or until browned, stirring to crumble. Add tomato sauce, 1/2 teaspoon salt and pepper. Cook for 2 minutes or until most of liquid evaporates.
Add pasta to beef mixture in pan, stirring to combine. Spoon pasta mixture into an 11 x 7-inch baking dish coated with cooking spray.
Place milk, flour, nutmeg, and remaining 1/2 teaspoon salt in a medium saucepan; stir with a whisk until blended. Cook over medium heat 2 minutes or until thickened, stirring constantly with a whisk. Add 1 cup cheese, stirring until smooth. Pour cheese mixture over pasta mixture; stir. Top evenly with remaining 1/2 cup cheese. Bake at 350° for 20 minutes or until lightly browned. Let stand 5 minutes before serving.