Bring a large pot of salted water to a boil. Add pasta and cook until 1 minute less than al dente, according to package directions. Drain, rinse with cold water to stop cooking, and drain well again.

Return the pot to medium heat. Melt butter. Whisk in flour, salt, mustard powder, black pepper, and cayenne pepper. Cook, whisking, for 1 minute until fragrant and lightly golden.

Gradually whisk in 4¾ cups of the half-and-half. Bring to a gentle simmer, whisking often, until heated through, about 2–3 minutes. Remove from heat, then add in cheddar cheese and Gruyere cheese. Stir until the cheese melts and the consistency is smooth.

Let the cheese sauce cool to room temperature. This step takes about an hour, but it's crucial because cooling the sauce helps prevent separation when refrigerated.

Stir cooled pasta into cooled cheese sauce until well coated. Spread evenly into a greased 9x13-inch baking dish. Cover tightly with foil and refrigerate for up to 2 days.

Remove dish from the refrigerator, then let it sit and come to room temperature.

Preheat oven to 400°F. Before baking, drizzle the remaining ¼ cup half-and-half evenly over the top to restore moisture absorbed during chilling. Bake, covered, for 45 minutes until hot and bubbling. Uncover and bake 10 minutes more, until lightly browned around the edges.

Let stand 10 minutes so the sauce can set a bit before serving. Serve hot.