In a medium saucepan over medium-high heat, saute butternut squash in olive oil, stirring occasionally until squash is very tender, about 8-10 minutes. Remove squash from pan to a small bowl and wipe pan clean.
In same saucepan, melt butter over medium heat then whisk in flour. Slowly add milk and half-and-half, whisking constantly until smooth and combined. Bring sauce to a low simmer over medium heat until sauce is thickened. Remove from heat and whisk in cheese, chipotle, nutmeg, and cooked butternut squash. Season sauce with salt and pepper to taste. Transfer sauce to a high-speed blender and blend on high speed until sauce is completely smooth.
Meanwhile, place pasta in a greased 9x13 baking pan. Pour sauce over top and stir to coat. Sprinkle cooked bacon on top and sprinkle breadcrumbs over all.
Bake mac 'n' cheese at 375F 15-20 minutes or until topping is golden and sauce is bubbly. Remove from oven and let stand 5 minutes, then serve hot. Enjoy!