Preheat the oven to 400°F (200°C). Pierce the sweet potatoes all over with a fork, set on a baking sheet, and bake until very tender when pierced, 45–60 minutes depending on size. Cool 10 minutes until safe to handle.
Meanwhile, prepare the filling: In a skillet over medium heat, melt 2 tablespoons of the butter. Add the diced apple, cinnamon, nutmeg (if using), and a pinch of salt. Cook, stirring, until the apple is just tender, 5–7 minutes. Stir in the maple syrup or brown sugar and the dried cranberries. Remove from heat.
Slice each potato in half lengthwise. Scoop the flesh into a mixing bowl, leaving a sturdy 1/4-inch shell. Add the remaining 1 tablespoon butter and the milk or Greek yogurt (if using). Mash until creamy; season with a little more salt to taste.
Fold the warm apple-cranberry mixture into the mashed sweet potatoes. Stir in the toasted pecans, if using.
Spoon the filling back into the potato shells, mounding slightly. Return to the baking sheet and bake at 375°F (190°C) until heated through and lightly browned on top, about 12–15 minutes. For deeper caramelization, broil 1–2 minutes, watching closely.
Serve warm. Optionally drizzle with a touch of maple syrup and sprinkle extra nuts for crunch.