How to Make It
Cut the butternut squash in half lengthwise, remove seeds and arrange the squash face down on a rimmed baking sheet. Pour about 1 cup of water into the baking sheet and bake until the squash is very tender when pierced with the tip of a knife, about 30 minutes. Remove from the oven and let cool (keep the oven on). When it is cool enough to handle, scoop out the squash into a bowl and mash it with a fork until smooth. Set aside.
Heat the 2 tablespoons of butter in a saucepan over moderate heat. Add the flour and cook, stirring until smooth, about 1 minute. Add the milk and cook over moderately low heat, stirring occasionally, until thickened, about 10 minutes. Whisk in the mashed butternut squash, then add the cheese and stir until completely smooth and melted. Season the sauce with salt and pepper, and keep it warm over very low heat.
Meanwhile, in a pot of boiling well-salted water, cook the pasta until al dente. Add the pasta to the cheese sauce and stir to coat completely. Pour it into the buttered gratin dish and top with the bread crumbs. Bake until bubbling and golden, about 30 minutes.