While the pasta is cooking, heat a skillet over medium high heat. Add two tablespoons of butter and cook the butternut squash until almost tender, about 6 to 8 minutes. Add the apple and fresh thyme leaves, continue to cook for another 2 minutes.
Heat a 2- to 3-quart saucepan over medium heat. Melt 4 tablespoons of butter and onions and sweat the onions for 2 to 3 minutes, until they start to soften but not brown. Add the flour and mustard powder, and cook for 2 minutes. Whisk in the milk, stirring constantly to avoid lumps. Stirring regularly, bring the sauce to a boil. Once it has boiled and thickened, remove the pan from the heat, add a pinch of nutmeg and stir in the grated cheeses, salt, and pepper.
In a large mixing bowl, combine the cooked pasta, squash mixture and cheese sauce. Transfer to a casserole or baking dish. Combine the remaining 2 tablespoons of butter (melted) with the breadcrumbs and parsley. Sprinkle the mixture evenly over top of the pasta. Cook in a 350˚ F oven for 15 to 20 minutes, or until bubbling around the edges.