Preheat the oven to 375℉. Cut the 1 butternut squash in half and place it on a lined or greased baking sheet, cut side down. Roast for about 45 minutes, until fork-tender. Remove from the oven, cool slightly, then scoop out the cooked flesh. Puree until smooth. Set aside.
While the squash is roasting, cook the 1 package pasta according to the package directions, then set aside in a large bowl.
Turn the oven down to 350℉ and butter or grease a 9x13-inch baking pan.
In a large saucepan over medium heat, melt the ¼ cup unsalted butter. Whisk in the ¼ cup sweet white rice flour and cook for about 2 minutes, whisking, until a paste forms. Whisk in the 1 cup whole milk, whisking constantly, until smooth, then whisk in the 1 ½ cups 2% milk until a smooth sauce forms. Cook, whisking often, until a thick sauce forms, about 5 minutes.
Remove the sauce from the heat and stir in 1 cup of the 2 cups shredded cheddar cheese and ½ cup of the 1 cup shredded mozzarella cheese until melted. Stir in the ½ teaspoon ½ teaspoon fine sea saltand ½ teaspoon black pepper.
Pour the cheese sauce onto the pasta in the bowl, and mix so that the pasta is coated with sauce. Stir in the pureed butternut squash. Spread half the pasta mixture in the prepared pan, then sprinkle with 1 cup of cheddar cheese and the remaining mozzarella cheese. Top with the remaining pasta mixture. Finish with the remaining ½ cup of cheddar cheese and sprinkle the top with ½ cup shredded parmesan cheese .
Place in the oven and bake for about 20-30 minutes, until the cheese is melted and the sauce is bubbling. Remove from the oven and let rest for 5-10 minutes before serving.
Notes
Don't overcook the pasta. Follow the instructions on your box of pasta, then cook for about 1-2 minutes less time so that the pasta is al dente (slightly firm). It will soften in the oven as it bakes and soaks up the sauce.
Rest after baking. Allow the baked mac and cheese to rest for about 5-10 minutes after it comes out of the oven so that it is not overly goopy.
Try different pasta shapes. You can use any kind of pasta shape here, though I prefer tubed or shaped "nooks and crannies" pasta like penne, ziti, or macaroni.
Add breadcrumbs. For a little crunch, mix 4 tablespoons of melted butter with ¼ cup of gluten-free or regular breadcrumbs, then scatter this mixture over the top of the pan. before baking.
Different cheese. These are my favorite cheeses to use, but feel free to try others. Gruyere is nice, and Jack cheese will add a mellow smoothness.
Try sweet potatoes! Swap the pureed butternut squash for about 1-2 cups of pureed sweet potatoes (depending on how much you want to add).
Or a different squash. All winter squashes are lovely here - try acorn squash, kabocha, or even pumpkin!