Preheat the oven to 400 degrees F (200 degrees C).
Peel, deseed, and dice the Butternut Squash (1).
Place the cubed squash on a baking sheet. Drizzle with 2 tbsp. Olive Oil (2 tablespoon) and toss with ½ tsp. Kosher Salt (to taste) ¼ tsp. Cayenne Pepper (1/4 teaspoon), and ¼ tsp. Ground Nutmeg (1/4 teaspoon). Roast in the oven for 30 minutes, or until the squash is golden brown, tossing halfway through.
Prepare Large Rigatoni (1 pound) according to package instructions, but undercook it by a couple of minutes so it is a bit shy of “al dente” (the noodles will soften more when they cook in the oven). Drain and set aside.
Chop the Bacon (12 ounce) into ½ inch pieces.
Dice the Onion (1) and chop the Fresh Thyme (2 tablespoon).
In a large skillet over medium heat, fry the chopped bacon until crispy. Drain on a paper towel-lined plate and reserve the rendered bacon grease.
Grate the Smoked Gruyere Cheese (8 ounce), Aged White Cheddar (8 ounce), and Gouda (8 ounce).
Sauté the onion in 2 tbsp. bacon grease and a pinch of salt until soft, about 5 minutes. Melt in 2 tbsp of Unsalted Butter (2 tablespoon)
When the butter is melted, whisk in the All-Purpose Flour (4 tablespoon) stirring constantly for 2 minutes, until the flour is toasted. Stir in the thyme.
In a steady stream, whisk in the Whole Milk (3 cup) until the sauce thickens.
Add the roasted squash to the sauce, mashing with a potato masher, wooden spoon, or a fork until almost completely smooth.
Stir in the Dijon Mustard (1 tablespoon) and remaining Cayenne Pepper (1/4 teaspoon) and Ground Nutmeg (1/4 teaspoon)
Stir in the grated cheeses (reserve about ¾ cup of the cheeses for the topping) until melted and smooth. Whisk in additional milk as needed to loosen the sauce.
Reduce the oven temperature to 375 degrees F (190 degrees C).
In a large bowl, combine the pasta, half the crisped bacon, and the sauce. Transfer the mixture to a greased baking dish.
Melt the remaining Unsalted Butter (4 tablespoon) and stir in the Panko Breadcrumbs (3/4 cup).
Sprinkle the remaining bacon over the dish, followed by the cheeses and then the breadcrumbs.
Transfer to the oven to bake for 20 minutes, until golden-brown and bubbling.