Position rack in center of oven and preheat to 350 degrees. Butter and flour two 9-inch diameter cake pans with 2 inch sides. Line bottom of each pan with parchment paper round. Whisk first 7 ingredients in a medium bowl. Using electric mixer, beat 1 cup butter in large bowl until fluffy. Add 1 1/4 cup sugar and 3/4 cup brown sugar and beat until smooth. Add eggs 1 at a time, beating well after each addition. Beat in vanilla, then bourbon, if desired (mixture may look curdled). Add flour mixture to egg mixture in 3 additions alternately with applesauce in 2 additions, beating until blended after each addition. Stir in apples and pecans. Divide batter between 2 cake pans and smooth tops.
Bake cakes until tester inserted in center of each comes out clean, about 50 minutes. Transfer cakes to racks and cool in pans 15 minutes. Cut around pan sides to loosen cakes. Invert cakes onto racks; peel off parchment paper. Place another rack atop 1 cake and invert again so that cake is rounded side up. Repeat with second cake. Cool completely. (Can be made 1 day ahead. Wrap each cake in plastic and store at room temperature.).
Frosting: Using electric mixter, beat cream cheese and butter in large bowl until smooth. Beat in vanilla extract and pinch of salt. Gradually add powdered sugar, beating until frosting is smooth and creamy, about 2 minutes.
Assembly: Using a long serrated knife, trim off rounded tops of cakes to make level; brush off any loose crumbs. Transfer 1 cake to platter, trimmed side up. Drop half of frosting (about 1 1/2 cups) by spoonfuls atop cake. Spread frosting evenly to edges of cake. Top with second cake, trimmed side down. Drop remaining frosting by spoonfuls on tops of cake, leaving sides of cake plain. Spread frosting to top edges of cake, swirling to make peaks, if desired. Sprinkle with pecans. Let cake stand at room temperature 1 hour to allow frosting to set slightly. (Can be made 1 day ahead. Cover with cake dome and refrigerate. Let cake stand at room temperature for at least 2 hours before serving.).