Bring 6 quarts of water to boil in a large pot. Add 2 tablespoons of salt. Cook the rigatoni in boiling water until tender, but not mushy, about 10 minutes. Drain, and then set aside.
Preheat oven to 400 degrees. On a sheet pan, toss butternut squash with olive oil, season with salt and pepper, and roast until tender when pierced with a fork, about 25-30 minutes. You want the squash to be almost falling apart tender. When it’s done, put the squash in a blender and puree it. You can also put the squash in a glass bowl and use an immersion blender. Set aside.
In a large Dutch oven, cook bacon until crisp. Remove the bacon with a slotted spoon and set aside. Add butter to the bacon fat, then sauté the onion and garlic until translucent. Add flour and stir well to combine to make roux. Slowly pour in the milk and half and half while constantly stirring, and bring mixture to simmer. The mixture will start to thicken. This is good. This is the base for the rich, cream sauce, so you want it lovely and thick.
Stir in the butternut squash puree. Cook on low heat until the mixture thickens even more, about 4-5 minutes. Add in 1 cup of the Gruyere, grate in the nutmeg and add the reserved bacon. Constantly stir until all of the cheese is melted. Add the mascarpone and mix until melted and combined. Stir in the chipotle and kale and add the cooked rigatoni. Toss pasta until it is well mixed.
Preheat your oven to broil. Sprinkle the bread crumbs and remaining cheese over the casserole. Place the Dutch oven on a rack 6 inches from the heating source. Broil for about 3-5 minutes, or until the topping is crunchy and golden.
Spoon portions into bowls and garnish with parsley.