Preheat oven to 375°F. Line a baking sheet with foil and place bacon slices in a single layer on lined baking sheet. Bake for 20 minutes or until crispy. Leave oven on. Remove bacon from oven and place on a paper towel to cool slightly. When cool enough to handle, chop into bite-size pieces.
Meanwhile in a large, deep skillet, heat 2 teaspoons of the extra virgin olive oil over medium-high heat. Add onions and 1/4 teaspoon salt and saute until onions begin to soften, about 4 minutes. Reduce heat to medium low and continue to cook until caramelized and brown in color, at least 30 minutes or up to an hour. When finished caramelizing, place in a bowl and set aside.
In the same pan, melt 2 tablespoons of butter. Whisk in flour and cook for 1 minute, whisking continuously. While whisking, add stock, milk, and pumpkin, nutmeg, cayenne, and dried mustard. Bring to a boil over medium-high heat. Reduce to medium and simmer until slightly thickened, 5-8 minutes. Remove from heat and stir in cheddar cheese until melted.
Meanwhile, bring a large pot of salted water to a boil and cook pasta as directed on package.
Drain pasta and return to pan. Pour cheese sauce over pasta and fold in onions and chopped bacon.
Spray a 2-quart casserole dish with non-stick cooking spray. Pour pasta into this dish. In a small bowl, combine pecorino cheese, Panko breadcrumbs and 1 teaspoon olive oil until everything is well coated with oil. Sprinkle evenly over the pasta. Cover with foil and bake at 375°F for 20 minutes. Remove foil and cook for another 35 minutes or until golden brown on top. Let rest 5 minutes prior to serving.