Preheat oven to 350 degrees. Spray a 13x9-inch baking dish with nonstick cooking spray.
Cook penne pasta al dente, according to package instructions. Drain and set aside.
Meanwhile, melt 2 tablespoons butter in a large skillet over medium heat. Add the onion and cook until tender, about 3-5 minutes.
Reduce heat to low and add the pumpkin puree, almond milk, cheddar cheese, 1/4 cup Parmesan cheese, nutmeg, thyme, salt, and pepper to the skillet. Stir to combine ingredients until cheese is melted and the sauce is smooth.
Add the drained penne and stir to evenly coat noodles in the sauce. Pour into prepared dish. Melt remaining 1 tablespoon butter in a small bowl and add panko breadcrumbs. Stir to combine and sprinkle evenly over top of the penne.
Bake uncovered for 20-25 minutes until heated through. Sprinkle with remaining 1/4 cup Parmesan and chopped parsley before serving.
Cook's Note: Cooked and crumbled sausage would be a wonderful addition to this casserole.