Preheat the oven to 375 degrees F.
Bring a large pot of salted water to a boil. Add the pasta and cook about a minute shy of the directions on the package, about 8 minutes. Drain well, reserving 1/2 cup of the cooked pasta water.
Meanwhile, heat the milk in a small saucepan, but don't let it boil.
Melt 6 tablespoons (reserving 2 tablespoons for the bread crumbs) of butter in a large (4-quart) pot and add the flour. Cook over low heat for 2 minutes, stirring with a whisk.
While whisking, add the hot milk and cook for a minute or two more, until thickened and smooth.
Off the heat, add the Gruyere, Cheddar, salt and pepper to taste and nutmeg. Add the cooked macaroni and the pasta water and stir well. Pour into a 3-quart baking dish.
Slice the tomatoes and arrange on top.
Melt the remaining 2 tablespoons of butter, combine them with the fresh bread crumbs, and sprinkle on the top.
Bake for 30 to 35 minutes, or until the sauce is bubbly and the macaroni is browned on the top.