Preheat broiler to high with oven rack in top third of oven. Place chiles on a baking sheet; coat with cooking spray. Broil in preheated oven until just blackened, about 10 minutes, turning once after 5 minutes; remove from oven. Transfer oven rack to middle of oven; turn oven temperature to 375°F. Transfer chiles to a bowl, and cover tightly with plastic wrap. Let stand at room temperature 15 minutes. Peel off and discard blackened skins from chiles; remove and discard stems and seeds. Tear chiles into 1/4-inch strips; set aside 1/3 cup strips. Place remaining chile strips in a mini food chopper or food processor; add oregano, and process until semi-smooth, about 10 seconds. Whisk together flour and 1/4 cup milk in a small bowl. Pour remaining 3/4 cup milk into a medium saucepan; bring to a boil over medium. Add flour mixture; cook, stirring constantly, until slightly thickened, about 2 minutes. Stir in chile-oregano mixture, salt, cumin, nutmeg, cayenne pepper, and 3/4 cup goat cheese. Remove from heat. Coat an 8-inch square glass or ceramic baking dish with cooking spray. Layer half of squash and potato slices in dish in alternating layers, beginning and ending with squash. Top with half of chile-cheese sauce. Repeat with remaining squash, potato slices, and sauce. Cover baking dish tightly with aluminum foil. Bake at 375°F on rack in middle of oven until squash and potatoes pierce easily with a knife, 50 minutes to 1 hour. Remove foil; sprinkle with almonds, reserved 1/3 cup chile strips, and remaining 1/2 cup goat cheese. Turn broiler to high; broil on middle rack until almonds are toasted and cheese is melted, 2 to 3 minutes. Remove from oven; let stand 20 minutes before slicing.