1. Heat oven and boil pasta: Heat oven to 375 degrees. Bring a large pot of water to a boil, then add salt generously and cook pasta 2 to 3 minutes less than manufacturer's instructions (the outside should be cooked but the inside underdone. Transfer to a colander, rinse under cold running water, and drain well.

2. Meanwhile, make bread crumbs: Tear bread into large pieces and pulse a few times in a food processor to form very large crumbs. Transfer to a bowl, and add melted butter. Toss evenly to coat.

3. Prepare baking dishes: Butter eight 6-ounce shallow baking dishes or one 1 1/2-quart baking dish.

4. Make cheese sauce: Melt butter in a 4-quart pot over medium heat, add onion, and cook, stirring occasionally, until translucent, about 5 minutes. Whisk in flour and cook, stirring with a wooden spoon, until bubbling but not browning, about 45 seconds. Add milk and whisk to combine. Bring to a simmer, stirring with a wooden spoon (scrape across the bottom and around edge of pot to prevent scorching), until thickened, about 4 minutes. Add fontina, 2/3 cup grated Gruyere, 1 2/3 cups grated cheddar, and 1/2 cup Parmigianno-Reggiano, stirring until completely melted and sauce is smooth. Season with salt and pepper, add cayenne and nutmeg, and stir to combine.

5. Assemble and add cheese topping: Add pasta to sauce and stir to thoroughly combine. Pour into prepared baking dishes and sprinkle evenly with the reserved cheeses, followed by the bread crumbs. If using, top with roasted tomato slices and thyme.

6. Bake: Place dishes on a parchment-lined baking sheet and bake until bubbling and cheese is golden brown, 25 to 30 minutes. Let cool 5 minutes before serving.