Preheat the oven to 400°F. Line a baking sheet with parchment paper or a silicone baking mat (for easy cleanup).
Place the cubed squash on the baking sheet. Drizzle with 1 tablespoon of olive oil and season with the cinnamon, nutmeg, and plenty of salt and black pepper. Toss to coat. Spread the squash in an even layer. Roast for 30 minutes, stirring once halfway through the cooking time, or until tender and slightly caramelized. Once you’ve removed the squash from the oven, increase the oven temperature to 425°F.
Meanwhile, heat a large skillet over medium-high heat. Add the sausage to the pan and cook for about 6 to 7 minutes, stirring and breaking up the meat into small pieces with a spatula, or until lightly browned. Transfer the sausage to a bowl and set aside.
Return the skillet to the stove. Reduce the heat to medium, and add 1 tablespoon of olive oil to the pan. When the oil is hot and shimmering, add the onion and cook for about 20 minutes or until very soft and lightly caramelized. (If the onions start to dry out at any point, add a splash of water to the pan.) Add the vinegar and maple syrup and cook for about 2 minutes or until the liquids are absorbed.
Transfer the roasted squash to a mixing bowl and roughly mash with a fork. (You don’t want it to be completely smooth—a few chunks are great for texture.) Taste and season with a little extra salt and pepper if needed.
Assemble your flatbreads! Place 2 pieces of naan onto each of two large baking sheets. Brush each flatbread with the remaining tablespoon of olive oil. Spread each with a relatively even layer of the butternut mash. Sprinkle with half the cheese, then top with the caramelized onions and sausage. Top with the remaining cheese and fresh sage. Bake the pizzas for 8 to 10 minutes at 425°F or until the cheese is melted and the flatbreads have crisped and browned on the undersides.
Slice each flatbread into 8-16 pieces (depending on your size preference). Serve warm or at room temperature.