Preheat the oven to 375 degrees.
Cook the macaroni according to the package directions. Drain well.
Meanwhile, heat the milk in a small saucepan until just simmering!
Melt 6 tablespoons of butter in a large pot and add the flour to make a roux. Cook over low heat for 2 minutes, stirring frequently, until golden brown. Carefully stream in the hot milk and cook for a minute or two more, until the milk starts to thicken. Remove from heat, add the shredded cheeses, thyme leaves, 1 teaspoon of kosher salt, freshly cracked black pepper, and nutmeg. Add the cooked macaroni and stir well. Pour into a 3-4 quart baking dish.
Melt the remaining 2 tablespoons of butter. Add the panko into the skillet and toss to combine, then sprinkle on the top. Bake for 30 to 35 minutes, or until the sauce is bubbly and the macaroni is browned on the top.