Preheat oven to 425 degrees. Place squash cubes and onions (if using) on a baking sheet and toss with 1 tablespoon olive oil. Season with salt and pepper. Roast until tender and golden brown, about 25-35 minutes.
Make the Spiced Skyr: Combine skyr, cumin and Aleppo pepper in a small bowl. Season with salt. Set aside.
Meanwhile, add remaining tablespoon of olive oil and sliced garlic to a nonstick skillet and heat over medium. Once garlic begins to sizzle, add kale and seaon with salt and pepper. Cook until kale is bright green and tender, about 3-5 minutes. Add a splash of water if kale is drying out and you would like it to cook some more.
Warm the flatbreads by placing them in the oven (either on a baking sheet or directly on the rack is fine) for a couple of minutes (if they are frozen, they can go straight from the freezer to the oven and be warm in just 3-4 minutes). Spread half of the yogurt mixture over one of the flatbreads. Top with kale and roasted vegetables. Sprinkle with pepitas. Serve. (You will have enough leftover roasted vegetables for another round of sandwiches).