Cook pasta according to package instructions. Drain pasta and rinse under cold water.
Position an oven rack to the center. Preheat the oven to 375ºF (190ºC). Grease a 9x13-inch baking dish with olive oil. Set aside.
Melt 2 tablespoons of butter in a sauté pan over medium-high heat. Add flour and stir immediately until a soft paste, or roux, forms. Add milk and begin to stir everything immediately to prevent the roux from clumping up too much.
Once the milk boils, reduce heat to medium-low and let the sauce simmer for about 3 to 4 more minutes, until the sauce thickens. Reduce the heat to low.
Add the oregano, thyme, black pepper and salt and stir. Add the butternut squash puree and mix until everything is incorporated. Mix in ⅔ cup of mozzarella, ⅔ cup of white cheddar. Save the rest of the cheese for topping later. Turn off the heat. Stir in the cooked pasta, until it's well coated with the butternut squash cheese sauce.
Pour mac and cheese into the prepared baking dish. Top with remaining mozzarella and white cheddar cheese. Bake for 20 minutes, then broil for about 3 to 4 minutes to brown the cheese on top. Check the mac and cheese after 3 minutes to see if it has been adequately browned.
