Preheat oven to 350 degrees F and grease a 3 qt baking dish (9x13"). Set aside.
Boil the pasta according to package instructions in heavily salted water. Cook for 1-2 minutes less than instructed. Drain and set aside, tossing once after a few minutes to avoid the noodles sticking together. Do not rinse.
While water is coming up to a boil, shred cheeses and toss together to mix, then separate out ⅓ of the shredded cheese to save for topping, leaving about ⅔ of the shredded cheese intended for mixing into the sauce.
Melt butter in a large pot over medium heat. Option to add aromatics here (see Note 1 for instructions if doing so). Once melted, sprinkle in flour and whisk to combine. Mixture will look like very wet sand. Cook for 1-2 minutes, whisking every so often. Slowly pour in about 1 cup of the milk, while whisking constantly, until smooth. Add the spices and whisk to combine. Slowly pour in the remaining milk, while whisking, until combined and smooth.
Pour in the pumpkin puree and whisk until combined. Continue to cook for about 1 minute.
Remove from the heat and, using a spatula, stir in about half of the cheese intended for mixing into the sauce. Mix until combined, then add the remainder of the cheese intended for the sauce. It’s okay if you still see some small chunks of cheese - this will create pockets of gooeyness in the end result.
Add the cooked pasta to the pot with the cheese sauce. Stir to combine fully, about 1-2 minutes.
Pour the pasta mixture into the prepared baking dish, then top with the remaining shredded cheese.
Bake for 30 minutes or until the cheese has melted and becomes bubbly. Option to leave under the broiler for the last minute. Serve and enjoy!