Preheat and Prep
Preheat your oven to 325°F. Line a 9×13-inch metal baking pan with parchment paper, leaving a generous overhang on the sides for easy lifting later. Spray the parchment lightly with nonstick spray.

Mix Dry Ingredients (Cookie)
In a medium bowl, whisk together the all-purpose flour, fine sea salt, baking soda, and baking powder. Set aside.

Cream Butter and Sugars
In the bowl of an electric mixer fitted with the paddle attachment, beat the cool room temperature butter, dark brown sugar, and granulated sugar until the mixture lightens in color and becomes fluffy, about 3 minutes. Scrape down the sides of the bowl.

Finish Cookie Dough
Beat in the eggs, one at a time, until smooth. Add the vanilla extract. On low speed, gradually add the dry flour mixture until combined. Finally, fold in the 1 1/4 cups of chocolate chips by hand. Place the dough in the fridge while you make the filling.

Make Cheesecake Batter
In a clean mixer bowl, beat the softened cream cheese and granulated sugar until completely smooth and creamy (about 3 minutes). Add the eggs one at a time, beating well after each. Scrape the bowl to ensure no lumps remain, then beat in the vanilla and salt.

Assemble the Base
Press about two-thirds of the chilled cookie dough evenly into the bottom of the prepared pan to form the crust. Pour the cheesecake batter over the dough and smooth it out.

Top the Bars
Take the remaining cookie dough, flatten small portions between your palms, and scatter them over the cheesecake layer. Gaps are okay! Sprinkle with the remaining 1/4 cup of chocolate chips.

Bake
Bake for 40 to 50 minutes. The edges should be golden brown, and the center should look set but slightly soft (it will firm up as it cools).

Cool and Chill
Remove from the oven and sprinkle with flaky sea salt if desired. Let the pan cool completely on a wire rack to room temperature. Transfer to the refrigerator and chill for at least 3 hours (or overnight) before lifting the bars out by the parchment paper and slicing.