Preheat the oven to 375 degrees F (190 degrees C). Line a baking sheet with parchment paper. Place butternut squash on the prepared baking sheet in a single layer. Bake in the preheated oven until fork-tender, about 20 minutes. Transfer butternut squash to a large bowl. Meanwhile, combine apples, brown sugar, onion, vinegar, turmeric, chile powder, cinnamon, cumin, ginger, and garlic powder in a saucepan over low heat. Cover and cook, stirring occasionally, until apples and onion are soft, 15 to 20 minutes. Add apple mixture to butternut squash in the bowl and stir gently to combine. Store in a covered container in the refrigerator.