Heat oven to 375°F. Grease a 9x13-inch baking dish.
Prep produce. Peel and cube squash; peel, core, and thinly slice apples. Toss apples with lemon juice.
Combine squash, apples, apple cider, cornstarch, 0.33 cup brown sugar, maple syrup, cinnamon, nutmeg, salt, vanilla, and 3 tbsp melted butter. Stir to coat evenly.
Spread the mixture in the prepared dish and cover tightly with foil.
Stir oats, flour, pecans, 0.25 cup brown sugar, and remaining 3 tbsp melted butter in a bowl. Fold in cranberries if using.
Bake covered for 25 minutes to begin softening the squash.
Uncover, scatter the oat-pecan topping evenly over the filling, and bake 25–30 minutes more until squash is tender and the top is crisp. Rest 10 minutes before serving.