Preheat your oven to 325°F (165°C). Line a 9×13-inch baking pan with parchment paper, leaving an overhang on the sides. Lightly grease the parchment paper. Combine graham cracker crumbs, ⅓ cup sugar, and ¼ teaspoon salt in a bowl. Pour in melted butter and mix until the mixture resembles wet sand. Press firmly into the bottom of your prepared pan. Bake for 10 minutes, then remove and cool slightly. Beat softened cream cheese with an electric mixer on medium speed until smooth, about 2-3 minutes. Add ½ cup sugar and beat until fluffy. Scrape down the sides of the bowl. Add eggs one at a time, mixing on low speed after each addition. Mix in vanilla extract, sour cream, and flour until smooth. Don’t overmix. Pour cheesecake filling over the pre-baked crust, spreading evenly. Tap the pan gently to release air bubbles. Bake for 25-30 minutes until the center is just set but slightly jiggly. Remove and let cool. In a medium saucepan over medium heat, melt 2 tablespoons butter. Add diced apples, brown sugar, cinnamon, nutmeg, cloves, and lemon juice. Cook for 8-10 minutes until apples are tender. Mix cornstarch with 1 tablespoon water and add to the pan. Stir for 1 minute until thickened. Remove from heat and cool for 10 minutes. Spoon the cooled apple mixture evenly over the cheesecake layer. Spread gently to cover the entire surface. Return pan to oven and bake for an additional 15 minutes. Remove and let cool completely at room temperature for 1 hour. Cover and refrigerate for at least 4 hours or overnight. Lift the dessert from the pan using parchment overhang. Place on a cutting board and cut into 16 bars using a sharp knife, wiping clean between cuts. Drizzle each bar generously with caramel sauce and sprinkle with sea salt flakes if desired. Serve chilled.