Heat oven to 350°F. Lightly coat 11“ x 7” baking dish with cooking spray.
Bring large pot lightly salted water to a boil. Add pasta and cook according to package directions; drain and rinse under cold water to stop cooking, then drain again. Return to pot.
Place bread into food processor and pulse into bread crumbs. Set aside.
Melt 1 Tbsp of the butter in medium saucepan over medium heat. Add onion and cook until softened, 6 to 7 minutes. Whisk milk, flour, mustard, and salt. Pour into saucepan and cook, whisking, until mixture begins to thicken, 3 to 4 minutes. Stir in cheeses and cook until melted, about 2 minutes. Pour over macaroni, add tomatoes, and mix well to coat.
Immediately pour into prepared baking dish. Melt remaining butter in medium nonstick skillet over medium heat. Add bread crumbs and cook, stirring, until coated with butter, about 1 minute. Sprinkle over macaroni and cheese.
Bake until bubbly and golden, 20 to 22 minutes.