Preheat your oven to 400°F (200°C) to ensure it is hot and ready for baking the butternut squash mixture.
In a large bowl, combine the cubed butternut squash, diced gala apples, ground cinnamon, vanilla extract, and brown sugar or honey. Stir everything together until the squash and apples are well coated with the spices and sweetener. Then add the salt and black pepper, mixing again to evenly distribute the seasoning.
Transfer the seasoned butternut squash and apple mixture into a lidded baking dish, spreading it out evenly. Place small pieces of butter over the top of the mixture to help it brown and become flavorful while baking. Cover the dish with its lid and place it in the preheated oven. Bake for 15 minutes.
After 15 minutes of baking, remove the dish from the oven. Uncover and add the golden raisins, dried cranberries, and chopped pecans or walnuts. Gently toss everything together with tongs or a spoon so the fruits and nuts are well distributed. Cover the dish again and return it to the oven. Continue baking for another 15 minutes, or until the butternut squash is tender and the top is lightly browned. For a little extra flavor, I sometimes sprinkle a tiny bit more cinnamon at this point.
Carefully remove the baking dish from the oven. Stir the baked mixture gently to ensure the melted butter and released juices are evenly distributed. Serve the warm butternut squash and apple medley straight from the dish for best flavor.