Preheat your oven to 350 degrees F. Grease a 9x13 inch baking pan and line it with parchment paper, leaving some overhang on the long sides so you can lift the bars out easily after baking.

Melt the butter in a light-colored saucepan over medium heat, stirring occasionally. Once it melts, keep cooking and swirling the pan every 30 seconds or so. After about 5 to 7 minutes the butter will foam, then the foam will settle and you will see small golden-brown bits forming on the bottom. It will smell nutty, almost like toffee. Pull it off the heat immediately and pour it into your large mixing bowl. Let it cool for at least 10 minutes until it feels warm but not hot when you hold your hand near the bowl.

Whisk both sugars into the warm brown butter until well combined. Add the pumpkin puree and whisk again. Add the eggs one at a time, whisking after each addition, then stir in the vanilla. The mixture should look smooth and slightly glossy.

Add the flour, pumpkin pie spice, cinnamon, baking powder, and fine salt directly to the bowl. Switch to a rubber spatula and fold everything together until just combined, meaning no dry streaks remain but you are not overworking the batter. Fold in 1 1/4 cups of the chocolate chips, saving the rest for the top.

Spread the batter evenly into your prepared pan. It will be thick, so use the spatula to push it into the corners. Scatter the remaining chocolate chips over the top and press them in gently.

Bake for 25 to 30 minutes. The bars are done when the edges are set and golden and the center no longer jiggles when you tap the pan. A toothpick inserted in the center should come out with just a few moist crumbs, not wet batter. Do not overbake or they will dry out.

Pull the pan from the oven and immediately sprinkle the flaky sea salt over the top. Let the bars cool completely in the pan, at least 1 full hour, before lifting them out and cutting into squares. Cutting too soon will give you a crumbly, messy edge.