Melt 6 tablespoons of the butter in a large stockpot over medium heat. When the butter is hot and bubbly, whisk in the flour.
Cook the flour and butter about 5 minutes, whisking occasionally to keep the roux smooth.
Pour in the warm milk and continue cooking over medium heat, whisking frequently until the sauce starts to thicken, about 10 minutes.
Reduce the heat to low then add 3 cups of the Fontina cheese, 1-½ cups of the Gruyere and 1 cup of the cheddar cheese along with the nutmeg, paprika, cayenne pepper, ½ teaspoon kosher salt, and black pepper.
While the cheese melts, cook the pasta in boiling water that has been salted with about a handful of kosher salt. Follow the suggested cooking time on the package of the pasta, taking care not to overcook. The pasta will continue to cook as it bakes in the oven.
Drain the cooked pasta and add it to the cheese sauce, stirring to coat and mix well.
Turn the cheese and pasta out into a 9” x 13” baking dish that has been sprayed with a cooking spray. Cover the top of the pasta with the reserved cheese.
Melt the remaining 2 tablespoons of butter in a skillet over medium heat. Toss in the panko breadcrumbs and cook until the crumbs are lightly brown, about 5 to 7 minutes, stirring frequently
Sprinkle the breadcrumbs over the top of the mac and cheese then bake in a 350-degree oven for 15 minutes until hot and bubbly.