Preheat the oven to 375°F (190°C) and lightly grease a 3-quart baking dish. Set aside.
In a large pot, bring water to a boil and add 1 teaspoon of salt. Add the pasta and cook for 4 minutes, leaving it very al dente. Drain and pour into the prepared baking dish; set aside.
In a large skillet over medium heat, cook the bacon until crisp, about 4-5 minutes on each side. Place on a paper towel-lined plate to drain excess oil, then chop into small pieces. Reserve half for garnish and set aside.
In a large pan, melt the butter over medium heat. Add diced shallots and sauté for 5-6 minutes until softened and nearly translucent. Add the minced sage and garlic, stirring for 1-2 minutes until fragrant.
Sprinkle the flour over the shallot mixture, stirring constantly, and cook for 1 minute. Gradually add the milk, whisking continuously to avoid lumps. Add the pumpkin puree, whisking until the mixture is smooth.
Continue whisking the mixture as it cooks, allowing it to thicken over approximately 5 minutes. Add the Dijon mustard, brown sugar, 1 1/4 teaspoons salt, cayenne pepper, onion powder, and black pepper, mixing well.
Lower the heat and incorporate the heavy cream. Fold in the grated cheeses, stirring until melted and smooth. Mix in half of the bacon.
Pour the cheese sauce over the pasta in the baking dish, stirring gently to coat the pasta evenly.
In a small bowl, mix the panko bread crumbs with olive oil until thoroughly coated. Sprinkle this mixture evenly over the top of the mac and cheese.
Cover the baking dish with foil and bake in the preheated oven for 12 minutes. Remove the foil, sprinkle the remaining bacon over the top, and bake uncovered for an additional 5 minutes until golden.
Garnish with extra sage, if desired, and serve warm.