Pre-heat oven to 350 degrees F.
Bring 4-6 quarts of water with ½ tablespoon salt to a boil in a large stockpot. Add pasta and return to a rapid boil. Cook uncovered stirring occasionally until pasta is al dente, about 6 minutes. Drain well and set aside.
In a small bowl, whisk together flour, dry mustard and nutmeg. In a large stockpot, melt 4 tablespoons butter over medium heat. Then add onions and a pinch of salt and sauté until onions are translucent, 5-7 minutes.
Add the flour mixture to the onions and cook for a few minutes until the fat is absorbed and you form a roux.
Then add in the two cups milk and bring to a simmer over medium-high heat. Simmer for 5-10 minutes until sauce is thick and smooth.
Add in black pepper, 3 cups cheddar cheese (reserve ½ cup for the topping) and Parmesan cheese and combine. Season to taste with salt.
Stir in pasta and mix until combined.
Spread the pasta in a 9x9 inch casserole dish.
In a separate bowl, combine Panko breadcrumbs and 2 tablespoons melted butter. Sprinkle remaining cheddar cheese and panko mixture over the pasta. Bake for 15-20 minutes (uncovered) until cheese is bubbly and the top is lightly browned. Let cool 5 minutes and serve.