Boil the macaroni according to package directions. Drain.
Sauté onion in butter until soft, about 5 minutes. Stir in flour and mustard and cook 2 minutes. Slowly whisk in milk. (Easier to do if you heat the milk first.) Cook until thick and bubbly. Do not boil though.
Turn down the heat and add 2 cups of cheese by the handful, stirring until melted. Stir in peppers. Mix with pasta.
Pour into a buttered 9x9 baking dish. Toss the remaining cup of cheese with bread crumbs and sprinkle over the top, then sprinkle with a dusting of paprika. If desired, top with sliced tomato. Broil till lightly browned.