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