Preheat the oven to 400°F (230°C). Oil a 7 by 11-inch (18 by 28cm) pan.
Coat the squash with 1 tablespoon of the olive oil, then spread it evenly on a rimmed baking sheet. Sprinkle with salt and pepper.
Bake for 30 to 35 minutes, until very tender and just starting to brown. Remove from the oven. Decrease the oven temperature to 350°F (175°C).
Meanwhile, heat the remaining tablespoon of olive oil in a small saucepan over medium-low heat. Add the garlic and sauté for 2 to 3 minutes, until just starting to brown. Add the coconut milk and ¾ cup (175ml) of the almond milk. Whisk in the nutritional yeast and arrowroot powder. Cook, whisking constantly, until nice and thick, about 5 minutes. Transfer the sauce to a large bowl and add the remaining ½ cup (120ml) of almond milk, the butternut squash, 1 teaspoon of salt, ¼ teaspoon of pepper, and the paprika, lemon juice, and miso. Stir to distribute the ingredients somewhat evenly. Working in batches, transfer to a blender or food processor and process until totally smooth and creamy.
Bring a pot of salted water to boil over high heat. Add a drizzle of olive oil to prevent sticking. Stir in the pasta and adjust the heat to maintain a low boil. Cook, stirring occasionally, until the pasta is al dente. Drain well and let cool briefly.
Put the pasta in a large bowl and add the vegetables. Add the sauce, using only 2 cups (475ml) of it if not adding the optional vegetables. Stir gently until thoroughly combined. Spread the mixture evenly in the prepared pan and scatter the breadcrumbs evenly over the top.
Bake for 20 minutes, until the top is golden. Serve right away.