Preheat oven to 375°F and lightly spray a 9×13-inch baking dish with cooking spray.
Peel, chop into large chunks, and boil sweet potatoes in water until fork-tender, about 15–20 minutes; drain, let cool slightly, then mash until smooth.
In a large bowl, combine mashed sweet potatoes with ½ cup melted unsalted butter, granulated sugar, eggs, whole milk, vanilla extract, ground cinnamon, ground nutmeg, and salt; stir until completely smooth.
Spread the sweet potato mixture evenly into the prepared baking dish.
In a separate bowl, mix all-purpose flour, packed light brown sugar, and chopped pecans; drizzle with 2 tablespoons melted unsalted butter and toss until crumbly.
Sprinkle the pecan streusel evenly over the sweet potato layer and bake for 25–30 minutes, or until the topping is golden brown and the filling is bubbly.
Let the souffle rest for 5 minutes before serving.