Preheat oven to 350°F (180°C). Line a 13x9-inch baking pan with foil, letting the foil extend over the sides for handles. Spray the foil with baking spray with flour.
Make the crust: In the bowl of a stand mixer fitted with the paddle attachment, beat 1 cup (227 grams) unsalted butter (softened) and ?cup (147 grams) firmly packed light brown sugar at medium speed until creamy, about 2 to 3 minutes, stopping once to scrape the bowl.
With the mixer on low, add 2 cups (250 grams) all-purpose flour and ½ teaspoon (1.5 grams) kosher salt. Mix just until combined and a crumbly dough forms.
Press the crust mixture evenly into the bottom of the prepared pan, using your hands or the bottom of a measuring cup to compact it.
Bake the crust on the middle rack until golden brown, about 20 minutes. Remove from oven and let the crust cool completely. Keep the oven on.
While the crust cools, prepare the apples: In a large bowl, combine 8 cups (900 grams) finely diced peeled Honeycrisp or Pink Lady apples, ½ cup (100 grams) granulated sugar, 1 teaspoon (2 grams) ground cinnamon, and ½ teaspoon (1 gram) ground nutmeg. Stir to combine.
Let the apple mixture stand at room temperature until the apples release most of their juices, about 45 minutes to 1 hour. After macerating, drain the apples in a sieve or colander and discard the liquid. Pat the drained apples lightly with paper towels if they seem very wet.
Make the cheesecake filling: In the bowl of a stand mixer fitted with the paddle attachment, beat 3 (8-ounce) packages (680 grams) cream cheese (softened), 3 large eggs (150 grams), 2 teaspoons (6 grams) vanilla extract, and the remaining ¾ cup (150 grams) granulated sugar at medium-high speed until smooth, about 2 to 3 minutes.
With the mixer on low, add 1 cup (125 grams) all-purpose flour to the cream cheese mixture and beat just until incorporated and smooth. Do not overmix.
Pour the cheesecake filling evenly over the cooled crust and gently spread to the edges.
Spread the drained apple mixture evenly over the cheesecake filling in a single layer.
Make the streusel topping: In a medium bowl, whisk together 1 cup (125 grams) all-purpose flour, ¾ cup (165 grams) firmly packed light brown sugar, ½ cup (50 grams) old-fashioned oats, ½ teaspoon (1.5 grams) kosher salt, and the remaining ½ teaspoon (1 gram) ground cinnamon.
Cut in ½ cup (113 grams) unsalted butter (softened) with a pastry blender, two forks, or your fingers until the mixture resembles coarse crumbs. Stir in ¾ cup (85 grams) chopped pecans.
Sprinkle the streusel evenly over the apples.
Bake on the middle rack until the center is set and an instant-read thermometer inserted into the center registers 160°F (71°C), about 45 minutes. Remove from the oven and cool completely in the pan on a wire rack.
Once cool, refrigerate the pan, uncovered, until thoroughly chilled, at least 8 hours or overnight.
Use the foil overhang to lift the bars from the pan. Transfer to a cutting surface and cut into bars. Serve chilled with Salted Caramel Sauce.