Preheat oven to 350 degrees F. Spray a 9 x 13-inch baking pan with nonstick cooking spray and set aside.
Heat the butter in a large, deep skillet over medium-low heat. Once hot, add the onions and cook for 5-10 minutes, until softened. Add the wine and continue cooking until onions are caramelized and golden brown, about 15 minutes.
To the onions, add the garlic and saute for 30-60 seconds or until fragrant. Add the pumpkin, chicken broth, milk, olive oil, salt, sage, nutmeg, and pepper; cook until heated through.
Meanwhile, bring a large pot of water to a rolling boil. Add the macaroni and cook until al dente, about 9-10 minutes. Using a large slotted spoon, remove the pasta to a strainer and run under cool water, reserving the pasta water.
To the pot with pasta water over medium-low heat, add the chicken. Cook for 8-10 minutes or until cooked through. Remove to a cutting board and chop into bite-sized pieces.
Add the pasta and chicken to the pumpkin sauce; stir well. Add ½ of the mozzarella cheese and gently mix. Transfer to the prepared baking dish and top with remaining mozzarella and Parmesan.
Bake for 15-20 minutes or until the cheese is melted and the sauce is bubbling. Let stand a few minutes before serving.