Preheat oven to 375 degrees F (190 degrees C). Bring a large pot of water to boil for the pasta.
Heat a large ovenproof skillet over medium heat. Add the Bacon (4 slice) and cook about 3 minutes, or until about halfway cooked. Add Yellow Onion (1) and continue cooking until bacon is crisp and onions are soft and translucent, about 4-5 minutes longer. Add Garlic (2 clove) and sauté 30 seconds longer.
Add the Dried Thyme (1/2 teaspoon), Butternut Squash (1) and Salt (3/4 teaspoon). Stir to combine and coat squash in bacon drippings. Slowly pour in Chicken Broth (1 cup), scraping the bottom of pan with a silicone spoon to loosen all the browned bits. Bring to a boil, cover, and reduce heat to a simmer. Cook for about 10 minutes or until squash is fork tender.
While squash is cooking, add Penne Pasta (12 ounce) to boiling water and cook according to the directions for al dente. If you are using gluten free pasta, cook it 5 minutes less than the package calls for al dente. It should be firm and a little crunchy. Drain and set aside.
Add the Half and Half (1 1/4 cup) and Parmesan Cheese (1/2 cup) to the squash mixture and stir. Add the cooked penne and gently stir to combine butternut squash sauce with pasta. If you aren't using an ovenproof skillet, transfer pasta with sauce to a greased baking dish. Top pasta with Shredded Mozzarella Cheese (1 cup).
Bake uncovered for 25 minutes, or until the butternut squash sauce is bubbling.
Cool for 5 minutes before serving.