Pre-heat oven to 375F. Drizzle olive oil and a dash of salt over the two butternut squash halves, then lay them flesh side down on a greased baking sheet. Roast in the oven for 30-35 minutes, until tender. Remove from oven and allow to cool before scooping out the flesh (about 3 cups). Keep oven on.
Cook the pasta according to package directions, stopping 1 to 2 minutes short of the recommended cooking time so that the pasta is al dente (about 4-5 minutes for our Pipe Rigate). Drain, return to pot, and set aside.
Make the butternut sauce:
Set large sauté pan with olive oil over medium heat. Add the onions and sauté, stirring occasionally, until soft and turning brown, 7-8 minutes. Add garlic and cook, stirring, for another minute. Add broth, stirring to loosen up the bits of onion at the bottom of the pan. Stir in the mustard, smoked paprika, salt, black pepper, and tamari. Simmer for 5 minutes and remove from heat.
In a blender, combine the 3 cups of roasted butternut squash, Greek yogurt, and sautéed onions with broth. Blend until smooth and creamy, adding more broth or water until it’s thick but pourable, like a béchamel sauce. It will thicken as it bakes!
Pour the butternut sauce over the pasta in the pot. Stir gently to combine. Pour into a 2-quart baking dish (approx. 8-inch by 8-inch). At this point, you could add the optional ingredients, such as shredded kale or sun-dried tomatoes.
Make the breadcrumb topping:
Add breadcrumbs to a small bowl along with the thyme, paprika, and salt. Mix to combine. Drizzle the olive oil over the breadcrumb mix and stir until combined. Spoon over the top of the pasta. Bake at 375F until bubbly and the breadcrumbs are golden brown, about 30-35 minutes.
Allow to cool slightly before serving. Garnish with fresh herbs and enjoy.