Preheat oven to 400°.
Cover a baking sheet with aluminum foil, and coat foil with cooking spray. Arrange tomato slices in a single layer on baking sheet. Drizzle oil over tomatoes. Sprinkle with thyme, 1/4 teaspoon salt, and garlic. Bake at 400° for 35 minutes or until tomatoes start to dry out.
Cook pasta according to package directions, omitting salt and fat. Drain well.
Place flour in a large Dutch oven; gradually add milk, stirring with a whisk until blended. Cook over medium heat 8 minutes or until thick and bubbly, stirring constantly with a whisk. Add cheddar, fontina, remaining 1/2 teaspoon salt, and pepper, stirring until cheese melts. Remove from heat. Stir in tomatoes and pasta. Spoon into a 13 x 9-inch baking dish coated with cooking spray. Combine grated Parmesan cheese, breadcrumbs, and paprika; sprinkle over pasta mixture. Bake at 400° for 25 minutes or until bubbly.