Preheat oven to 350°F. Butter a 9-inch square glass baking dish.
Cook macaroni; drain and set aside.
Grate cheese; reserve ½ cup for topping and set rest aside for sauce.
Melt 3 tablespoons butter in 3 quart saucepan over medium heat. Add red pepper and onions. Sautee onions until limp and slightly brown.
Blend in flour and cook an additional minute.
Stir in pumpkin puree, milk, salt and thyme; cook until sauce thickens.
Stir in 2 cups grated cheese.
Combine sauce and prepared macaroni; place into prepared baking dish.
Melt 2 tablespoons butter and combine with Panko bread crumbs; stir in ½ cup cheese. Sprinkle over top of macaroni mixture.
Bake 35 to 40 minutes or until surface has browned slightly and sauce begins to bubble.
You can make the sauce ahead of time and then blend it with cooked macaroni when you’re ready. Or, you can assemble this casserole the night before so its ready to bake on a busy evening.