Cook macaroni as directed on package, omitting salt.
Meanwhile, melt butter in large saucepan on low heat. Add onions; cook and stir 3 to 5 minutes or until crisp-tender. Whisk in flour and mustard; cook 2 minutes. Gradually whisk in milk until blended; cook on medium heat 3 to 5 minutes or until thickened, whisking constantly. Add 2 cups cheese; cook 1 minute or until melted, stirring constantly.
Drain macaroni. Add to sauce; stir to evenly coat. Stir in tomatoes. Pour into 8-inch square baking dish sprayed with cooking spray; top with remaining cheese.