Preheat oven to 400°F. Spray a 9x13-inch casserole dish with nonstick spray.
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 for 35 minutes or until tomatoes start to dry out. Keep oven preheated.
Cook pasta according to package directions. 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 the prepared casserole dish. Combine grated parmesan, breadcrumbs, and paprika; sprinkle over pasta mixture.