Preheat oven to 350 degrees. In a medium skillet, heat oil over medium-high. Add onion, garlic, butternut squash, and pancetta and cook, stirring occasionally, until onion is soft and vegetables begin to brown, 5 minutes. Add sage and red-pepper flakes, season with salt and pepper, and cook, stirring, 1 minute.
In a large bowl, combine pork, cheese, bread, and egg. Add vegetable mixture and season with 2 teaspoons salt and 1/2 teaspoon pepper. Using your hands, mix until ingredients are combined. Transfer to a parchment-lined rimmed baking sheet; form into a 4-by-10-inch loaf. Bake until meatloaf is cooked through, 40 minutes, rotating sheet halfway through. Let rest 15 minutes before slicing.