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