Heat oven the 425ºF.
Bring a large pot of water to a boil. Add the squash and cook until very soft, about 10 minutes.
While the squash cooks, melt the butter in a large pan. Whisk in the flour and cook 1 minute, or until golden brown. Whisk in the milk, ensuring there are no lumps. Simmer for 2-3 minutes, or until the sauce thickens slightly. Whisk in the mustard powder and cayenne pepper; remove from heat.
Use a slotted spoon to transfer the cooked squash into the cream sauce, leaving the water behind. Mash the squash into the sauce to create a smooth mixture.
Add the pasta to the water you used to cook the squash. Cook until al dente (cooking time with vary depending on the brand of pasta used; follow the guidelines on the box.)
Stir 1 cup of the pasta cooking water into the cream sauce. Drain the pasta and add to the sauce. Stir in the cheese. Season to taste with salt and pepper.
Transfer the mac and cheese to a 9x6 inch baking pan. In a small bowl, mix the pretzel crumbs and olive oil. Spread over the macaroni and cheese.
Bake 15 minutes.