Position oven rack to lowest setting. Preheat oven to 400°.
Place squash, cut sides down, on a foil-lined baking sheet coated with cooking spray. Bake at 400° 30 minutes or until squash is tender. Cool slightly, and peel. Mash pulp to measure 2 1/2 cups. Combine the pulp and milk in a food processor; process until smooth. Add granulated sugar and next 5 ingredients (through cloves); process until smooth.
Increase oven temperature to 425°
Lightly spoon flour into a dry measuring cup; level with a knife. Combine flour and brown sugar in a medium bowl; cut in butter using two knives or a pastry blender. Add pecans; toss to combine.
Roll dough into a 13-inch circle; fit into a 9-inch deep-dish pie plate coated with cooking spray. Fold edges under; flute. Pour squash mixture into prepared crust. Place pie plate on bottom rack; bake at 425° for 15 minutes. Remove pie from oven.
Reduce oven temperature to 350°.
Sprinkle flour mixture evenly over filling; shield edges of piecrust with foil. Return pie plate to bottom rack; bake an additional 40 minutes or until center is set. Cool on a wire rack. Garnish each serving with 1 tablespoon whipped topping, if desired.