Move the oven rack to the middle position. Pre-heat oven to 350°F/180°C/Gas Mark 4. Apply cooking spray to a casserole dish. Set aside.
Follow directions on the package to cook pasta. Drain and rinse.
Heat olive oil in a sauté pan over medium heat. Cook crushed garlic for 30 seconds. Add butternut squash cubes and stirring frequently until lightly browned (about 3 minutes).
Add 2 tbsps of water, cover the pan and let cook. Add more water when it evaporates as many times as needed until the butternut squash is tender (about 10 minutes). Season with salt and pepper. Use a food processor or an immersion blender to make a smooth butternut squash-garlic puree. Transfer to a bowl; clean the pan.
Melt butter in the pan over medium-high heat. Stir in flour to get a soft paste. Add milk,stir immediately to help the paste dissolve evenly.
Bring milk to boil, reduce heat to medium-low and add butternut squash puree. Stir well, add thyme and oregano stir again. Reduce heat to low; add ¾ cup of mozzarella, ¾ cup of cheddar, mix well. Season with salt generously. Turn off the heat, add penne pasta and stir to coat well.
Pour the mac’n’cheese into the baking pan, top with mozzarella, cheddar and parmesan. Bake for about 15 minutes, turn on the broiler and broil the casserole for 4 minute until browned.