Cook beef, onion, and carrot in a large nonstick skillet over medium-high heat until browned, stirring to crumble. Drain well; return meat mixture to pan. Add tomatoes, 1/2 teaspoon salt, 1/4 teaspoon pepper, and next 4 ingredients; bring to a boil. Reduce heat, and simmer, uncovered, 28 minutes or until liquid evaporates, stirring occasionally.
Cook pasta according to package directions, omitting salt and fat.
Combine milk and next 3 ingredients in a large, heavy saucepan. Cook over medium-high heat to 180° or until tiny bubbles form around edge (do not boil). Remove from heat. Cover; let stand 10 minutes. Strain mixture through a sieve into a bowl; discard solids. Set milk mixture aside.
Preheat oven to 375°.
Melt butter in a large saucepan over medium-low heat. Add flour, stirring well with a whisk. Cook 1 minute, stirring constantly. Gradually add milk mixture, stirring well with a whisk; cook over medium heat until thick (about 10 minutes). Stir in 1/2 teaspoon salt, 1/4 teaspoon pepper, and nutmeg. Remove from heat; stir in 1/2 cup cheese. Reserve 1 1/2 cups sauce.
Combine pasta and remaining cheese sauce. Spoon half of pasta mixture into a 13 x 9-inch baking dish coated with cooking spray. Spoon meat mixture over pasta. Top with remaining pasta mixture. Pour reserved cheese sauce evenly over pasta layer. Sprinkle with 1/4 cup cheese.
Bake at 375° for 25 minutes or until bubbly. Let stand 10 minutes before serving.