Place an oven rack in the center position and preheat the oven to 350°F (175°C). Lightly spray a 9x13-inch metal baking pan with nonstick cooking spray, line with parchment paper leaving a 2-inch overhang on the long sides, and spray the parchment lightly.
Add the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice to a medium bowl. Whisk for about 30 seconds until evenly distributed, then set aside.
Pour the cooled melted butter into a large mixing bowl and add the granulated sugar and packed brown sugar. Whisk vigorously for about 1 minute until glossy and thick, breaking up any lumps.
Crack the eggs into the butter mixture one at a time, whisking until fully combined and slightly lighter in color. Stir in the vanilla, then add the pumpkin puree and whisk for 30 to 45 seconds until uniform with no white streaks.
Add half of the flour mixture and fold gently with a silicone spatula until most of the flour disappears. Add the remaining flour mixture and fold until just combined, stopping as soon as no dry flour remains.
Measure out 1 1/4 cups of the semi-sweet chocolate chips and fold them into the batter 6 to 8 times until evenly spread. Set aside the remaining 1/4 cup of chips for the top.
Scrape the batter into the prepared pan and spread into an even layer, pushing it into the corners. Sprinkle the reserved 1/4 cup of chocolate chips over the top, press them lightly into the surface, and add a small pinch of flaky sea salt if desired.
Bake for about 28 minutes, checking at 25 minutes. The edges should be set and lightly golden and the center should spring back gently; a toothpick should come out clean or with a few moist crumbs. Rotate the pan halfway through if your oven has hot spots.
Transfer the pan to a wire cooling rack and cool for 20 minutes. Use the parchment overhang to lift the slab out of the pan and cool for another 20 to 30 minutes until the center firms up and the chocolate sets slightly.
Move the cooled slab to a cutting board and cut 4 rows by 6 rows for 24 bars, wiping the knife clean every few cuts. Serve at room temperature, or warm briefly if you like the chocolate soft and gooey.