Bring a pot of water to a boil, season with salt and cook the macaroni to al dente.
Pre-heat the broiler and place a rack in the middle of the oven.
Heat the EVOO in a saucepot over medium heat. Sauté the onions and garlic until soft, 6-7 minutes, and stir in the thyme.
Scoot the onions off to the side of the pan and melt the butter. Whisk the flour into the butter and combine, about 1 minute. Whisk in the stock and milk, then season the sauce with salt, pepper and nutmeg and cook until thickened, about 3-4 minutes.
Stir in the defrosted butternut squash and a few dashes of hot sauce. Reduce the heat. When the sauce comes to a bubble, stir in the Parmigiano Reggiano cheese. Combine the sauce and macaroni, transfer to a casserole dish and top with the shredded yellow cheddar cheese, parsley and paprika. Brown the macaroni under the broiler, 4-5 minutes, until brown and bubbly.
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