Preheat the oven to 375 degrees.
Cook the macaroni according to the directions on the package. Drain well.
Meanwhile, heat the milk in a small saucepan, but don’t boil it!
Melt 6 tablespoons of butter in a large 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. Remove from heat, add the Gruyère, Cheddar, thyme, 1 teaspoon salt, pepper, and nutmeg. Add the cooked macaroni and stir well. Pour into a 3-quart baking dish.
Melt the remaining 2 tablespoons of butter, combine them with the panko 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.