Bring a large pot of well-salted water to a boil. Cook the pasta until al dente according to package directions. Drain and set aside.
In a large saucepan or Dutch oven, melt the butter over medium heat. Whisk in the flour and cook for 1 to 2 minutes, stirring constantly, until golden and slightly nutty.
Slowly whisk in the warm milk, a little at a time, until smooth and thickened, about 5 minutes. Stir in the pumpkin purée, Dijon mustard, smoked paprika, nutmeg, salt, and pepper.
Reduce the heat to low. Stir in the Gruyere and sharp white cheddar until melted and creamy. Taste and adjust seasoning if needed.
Add the cooked pasta to the sauce, stirring until evenly coated. Transfer the mixture to a greased 9x13-inch baking dish.
In a small bowl, mix together the panko, melted butter, Parmesan, and thyme. Sprinkle evenly over the pasta.
Bake at 375°F for 20 to 25 minutes, until bubbly and golden brown on top.
Let cool for 5 minutes before serving.