Preheat oven to 400F and lightly grease a 9-inch baking dish. Set aside.
Bring a medium pot of water to a boil over high heat. Reduce heat to medium, add butternut squash, and allow squash to simmer 8-10 minutes until tender when pierced with a fork. Drain squash, transfer to a bowl, and lightly mash with a fork into a semi-chunky mash. Set aside.
Arrange bacon in a single layer in a large skillet over medium heat. Cook bacon 8-10 minutes, turning occasionally until bacon is crispy. Drain bacon on paper towels then finely chop.
Set pan with bacon drippings over medium heat and melt 2 tablespoons butter. Whisk flour and garlic into drippings and cook 1-2 minutes until golden-brown.
Slowly drizzle in milk and cream, whisking constantly until smooth and incorporated. Cook sauce over medium heat, stirring occasionally until sauce is bubbly and thickened. Remove from heat and add chipotle and both cheeses, stirring until cheese is melted.
Fold cooked pasta, butternut squash, and bacon into sauce and season with salt and pepper to taste. Scrape pasta into prepared baking dish and set aside for a moment.
In a small bowl, combine breadcrumbs and melted butter. Sprinkle evenly over mac and cheese.
Bake mac and cheese at 400F 15-20 minutes until sauce is bubbly and breadcrumbs are golden-brown. Serve mac and cheese warm and enjoy!