Roast 2 cups peeled, cubed butternut at 400°F with a drizzle of oil and pinch of salt for 20–25 minutes until very tender. Or steam until soft. Purée in a blender with a splash of milk until silky.
Boil in well-salted water until just shy of al dente. Reserve 1/2 cup pasta water, then drain.
In a large pot, melt 3 tablespoons butter over medium heat. Stir in flour and cook 1–2 minutes until it smells toasty, not burnt.
Slowly whisk in milk (and broth if using). Simmer 3–4 minutes, stirring, until thick enough to coat a spoon.
Add garlic, onion powder, Dijon, nutmeg, 1 teaspoon salt, and several grinds of black pepper. Whisk in the butternut squash purée until smooth and glowing.
Off heat (important to avoid grainy sauce), stir in cheddar and Parmesan until melted and glossy. As Serious Eats explains, keeping the heat low when adding cheese prevents the proteins from tightening up and going grainy. Adjust thickness with reserved pasta water as needed.
Fold in the pasta until every curve is coated. Taste and tweak salt/pepper. If it seems sweet, add a pinch more salt and a whisper of Dijon.
For a crispy top, transfer to a buttered 9×13 dish. Mix panko with melted butter and smoked paprika; sprinkle over. Bake at 425°F for 8–10 minutes until golden.
Garnish with chives, cracked pepper, or a pinch of chili flakes. Try not to inhale it in one sitting.