Heat oven to 350°F. Grease a 2-quart baking dish.
Boil sweet potato chunks in water until tender, 15–18 minutes.
Drain well, then mash until smooth and steamy.
Whisk melted butter, both sugars, milk, vanilla, salt, cinnamon, and nutmeg.
Beat in the eggs until fully blended.
Fold the mash into the custard mixture until velvety.
Spread into the prepared dish and smooth the top.
Stir pecans, brown sugar, flour, and salt; drizzle in melted butter.
Toss until sandy clumps form; scatter evenly over the filling.
Bake until puffed and set at the center, 25–30 minutes.
Rest 10 minutes before serving warm.