Boo's Butternut Squash Mac-n-Cheese

From Rachael Ray: 365 No Repeats

Coarse salt
1 pound macaroni with ridges, such as tubettini or mini penne rigate
2 Tbsp extra virgin olive oil (EVOO)
2 Tbsp unsalted butter
2 Tbsp chopped fresh thyme, plus a few sprigs for garnish
1/2 medium onion
3 Tbsp all-purpose flour
2 C chicken stock or broth
1 10oz box frozen cooked butternut squash, defrosted
1 C cream or half-and-half
2 C grated sharp cheddar cheese
1/2 C grated Parmigiano-Reggiano
1/4 tsp nutmeg
Fresh ground black pepper to taste

Heat a pot of water to boil for the pasta. Salt the water, then add the pasta and cook al dente. While the pasta cooks, heat a medium heavy-bottomed pot over medium heat. Add the EVOO and butter. When the butter melts into the oil, add the thyme and grate the onion directly into the pot with a hand-held grater or microplane. Cook the grated onions for a minute or 2, then add the flour and cook together for a minute or 2 more. Whisk in the stock, then add the butternut squash and cook until warmed through and smooth. Stir in the cream and bring the sauce to a bubble. Stir in the cheeses in a figure-eight motion and season the completed sauce with salt, nutmeg, and pepper. Taste to adjust seasonings.
Drain the cooked pasta well and combine with the sauce.