Preheat the oven to 400 degrees. Line a baking sheet with aluminum foil. Cut the sweet potato into ½ to 1-inch chunks and toss with the olive oil. Season with the salt and pepper. Spread onto the prepared baking sheet and set aside. Cut the apple into ½ to 1-inch chunks and set aside. Bake the sweet potatoes for 25-30 minutes. At the last 15 minutes of cooking time, spread the apple chunks over the sweet potato and add the cinnamon. Toss to combine and continue baking until tender. Layer the cottage cheese, roasted sweet potato, roasted apple, dried cranberries, pomegranate seeds, pumpkin seeds, almonds, and coconut flakes in a bowl.