Cut each squash in half crosswise; scoop out seeds. Cut a thin slice off the bottom of each half so it can stand upright. Place each half, cavity side down, in a 9- by 13-inch baking pan and cover pan tightly with foil. Bake in a 350° regular or convection oven until tender when pierced, 45 to 50 minutes.
Meanwhile, in a 10- to 12-inch nonstick frying pan over medium-high heat, stir sausage until it is crumbly and just slightly pink, about 5 minutes. Drain off and discard fat. Add onion, apples, raisins, cranberries, and thyme; stir often until apples are tender when pierced, 8 to 10 minutes. Stir in pecans.
Uncover squash and turn halves upright; fill equally with sausage mixture. Drizzle equally with maple syrup and bake, uncovered, until filling is slightly browned on top, about 15 minutes longer.
Nutritional analysis per main-dish serving.