Bring a large pot of water to a boil; add salt. Cook the macaroni for 1 minute less than the timing listed on the package instructions. Drain the macaroni and set aside.
Preheat the oven to 450 degrees F. Grease a 9-by-13-inch baking dish with butter; set aside.
In a large skillet or saucepan, melt the butter over medium heat. Add the onion with a pinch of salt and cook, stirring occasionally until soft, 4 to 6 minutes. Stir in the cayenne, paprika, nutmeg and several turns of black pepper and cook for 2 minutes. Increase the heat to medium-high, whisk in the flour and cook for 1 minute. Add 3 cups of the milk and cook, stirring and whisking frequently, until thickened, 3 to 5 minutes; repeat with the remaining 3 cups milk. (I like to use a whisk if I see any lumps. Otherwise, I stir with a spoon or spatula.) Add the Brie and Gruyère, stirring until the cheese is completely melted. Take the skillet off the heat and stir in the cooked macaroni. Season to taste with salt and pepper.
Transfer to the prepared baking dish. Sprinkle the top with the panko and Parmesan. Bake until golden brown on top, about 15 minutes.
Allow to cool for a few minutes. Serve with a bar of ingredients on the side for your guests to choose!