Preheat the oven to 400 degrees, grease a 13x9 baking dish and set aside.
Coat the diced squash in 1 tablespoon of olive oil, and place on a large baking sheet. Sprinkle with salt and pepper, and roast the squash for about 30 minutes until it begins to become brown on the edges. Let squash cool, and reduce the oven temp to 350.
Bring a large pot of water to a boil, and cook pasta until al dente, about 2 minutes less than the box recommends. Drain, and set pasta aside.
In another large pot, heat 1 tablespoon of olive oil and sauté the onion and garlic for 5 minutes until they become soft. Whisk in the corn starch, nutritional yeast, and almond milk, and miso paste together for 5 minutes until the mixture begins to thicken. Add in the roasted squash and use an immersion blender to puree into a smooth sauce, adding more almond milk if needed if the sauce is too thick. Taste, and add salt and pepper, using more if desired.
Add the sauce to the pasta, and stir well to combine. Pour the pasta/sauce mixture into the greased baking dish. Top with gluten free bread crumbs, and place in the oven (uncovered). Bake for 20 minutes until the breadcrumbs begin to brown and the pasta starts to bubble. Serve hot, and cover any leftovers for a up to 3 days in the refrigerator.