Heat oven to 375°F. Lightly butter a 3-quart baking dish.
Bring a large pot of water to a boil. Stir in 2 tbsp kosher salt.
Cook macaroni until just shy of al dente. Drain and set aside.
Melt 7 tbsp butter in the empty pot over medium heat.
Whisk in flour and cook, whisking, for 2 minutes to make a roux.
Slowly pour in warm milk, whisking, until smooth. Simmer until thick, 4–5 minutes.
Season with 1 tsp kosher salt, pepper, and nutmeg. Take off heat.
Stir in cheddar and Gruyère until fully melted and creamy.
Fold the drained macaroni into the cheese sauce until coated.
Melt remaining 3 tbsp butter. Toss with bread crumbs to moisten.
Spread pasta in the dish. Add tomato slices over the top, if using.
Cover evenly with buttered crumbs. Bake until bubbling and golden, 25–30 minutes.
Rest 5 minutes before serving for cleaner scoops.