Preheat oven to 425°.
Peel, seed and cube butternut squash.
Place in a well-sprayed 10x15” glass baking dish.
Sprinkle with at least a ½ tsp. each of salt, pepper and rosemary.
Drizzle a few tablespoonfuls olive oil over top.
Bake at 425° for about 45 minutes until squash is done.
Meanwhile, fry bacon in a large skillet.
Once cooked, place bacon on paper towels to absorb extra grease and cool.
Break bacon pieces into ½” pieces and set aside.
Reserve about 1/3 cup of the bacon grease.
Add shallots and garlic to bacon grease in pan and sauté until tender.
Stir in flour and continue whisking for about 30 seconds.
Slowly add whipping cream, about 1/8 cup at a time until all is incorporated.
Add remaining salt, nutmeg, and pepper, to taste.
Check seasonings.
Add more salt and pepper if desired.
Cook over low-medium heat until thickened.
Bring water to a boil in a large stock pot.
Add penne pasta and cook according to package directions.
Drain.
Turn off heat in the skillet containing the cream sauce.
Add the pasta and stir to combine.
Once the butternut squash is cooked, remove about one fourth of the squash and set it aside in a bowl.
To the remaining three-fourths of the butternut squash in the 10x15” glass baking dish, add all of the pasta/cream mixture, three-fourths of the bacon, and three fourths of each of the cheeses.
Stir well to combine.
Sprinkle top with remaining one-quarter butternut squash, remaining one-quarter bacon, and remaining cheeses.
Add more cheese, if desired.
Bake at 425° for about 15-20 minutes until hot and bubbly.
Tent with foil, if necessary to avoid over-browning.