Preheat oven to 350 degrees F (175 degrees C). Line a 9x13-inch baking dish with parchment paper, and lightly grease the paper.
Beat spice cake mix, 1 can apple pie filling, eggs, and vegetable oil with an electric mixer on medium speed for 2 minutes in a large bowl.
Pour batter into the prepared baking dish and bake in the preheated oven until a toothpick inserted into the center comes out clean, about 30 minutes. Cool in the pans for 10 minutes before removing to cool completely on a wire rack. Slice in half horizontally to create two layers.
Whisk milk, cream, French vanilla pudding mix, butterscotch pudding mix, cinnamon, and nutmeg for 2 minutes in a large bowl. Transfer to refrigerator to chill.
Place one layer of cake in the bottom of a large 8-quart rectangular plastic container. Poke holes in the cake with a skewer or toothpick and pour 1 cup caramel ice cream topping over the top of the cake. Sprinkle 1/3 cup pecans over the caramel and spread half of the pudding mixture on top.
Spoon 1 can apple pie filling over pudding mixture and spread 1 container whipped topping over the filling. Place second cake layer on top of whipped topping and repeat the layering process.
Drizzle assembled trifle with remaining 1/4 cup caramel topping and sprinkle with remaining 1/3 cup pecans. Refrigerate until serving.