Prepare Pan and Oven:
Preheat oven to 350°F (175°C). Line a 9x13 inch baking pan with parchment paper, leaving overhang on the sides.
Make the Graham Cracker Crust:
In a medium bowl, combine graham cracker crumbs, sugar, cinnamon, flour, and salt. Pour in melted butter and stir with a fork until mixture resembles wet sand.
Press mixture firmly into the bottom of prepared pan using the bottom of a measuring cup to create an even, compact layer.
Bake for 10-12 minutes until lightly golden and fragrant. Remove from oven and let cool while preparing other components.
Prepare the Crumble Topping:
In a small bowl, mix together flour, both sugars, cinnamon, and salt. Add melted butter and stir with a fork until mixture forms clumps. Place bowl in refrigerator to chill.
Make the Cheesecake Filling:
Using a hand mixer or stand mixer with paddle attachment, beat softened cream cheese on medium speed until completely smooth, about 2 minutes.
Add sugar and beat for another minute until light and fluffy.
Add sour cream and vanilla extract, beating just until combined.
Add eggs one at a time, beating on low speed after each addition just until incorporated. Do not overmix. Scrape down bowl sides as needed.
Prepare the Apple Layer:
Peel and dice apples into ¼ to ½ inch pieces.
In a medium bowl, toss diced apples with brown sugar, cinnamon, nutmeg, and ginger until evenly coated.
Assemble and Bake:
Pour cheesecake filling over cooled crust and spread into an even layer using an offset spatula.
Spoon spiced apples evenly over cheesecake layer, distributing uniformly.
Remove crumble topping from refrigerator and sprinkle evenly over apples.
Bake for 40-45 minutes until edges are set and center has just a slight jiggle. Crumble topping should be golden brown. If topping browns too quickly, tent pan with aluminum foil.
Cool and Chill:
Let bars cool in pan on a wire rack for about 1 hour until room temperature.
Cover pan and refrigerate for at least 4 hours, or overnight for best results.
Use parchment paper overhang to lift entire slab out of pan. Place on cutting board and cut into 16 bars using a sharp knife, wiping clean between cuts.
Serve chilled with optional toffee or caramel sauce drizzle.