Heat the oven to 350°F. Line an 8-inch square pan with parchment, leaving a 2-inch overhang on two sides for easy lifting. Lightly grease the parchment and sides.
Toast the pecans on a small baking sheet in the preheating oven for 6–8 minutes until fragrant; cool slightly, then roughly chop if not already chopped.
Make the crust: In a bowl, combine flour, granulated sugar, and fine sea salt. Stir in the melted butter until the mixture looks like damp sand and holds when pressed. Press firmly and evenly into the prepared pan. Dock a few times with a fork, chill 10 minutes, then bake 12–15 minutes until the edges are just turning pale golden.
While the crust bakes, whisk the filling: In a large bowl, whisk the eggs and egg yolk until lightly foamy. Add brown sugar, espresso powder, and fine sea salt; whisk until smooth. Whisk in dark corn syrup, vanilla, and bourbon. Stream in the melted butter, whisking constantly until glossy, then whisk in the flour just until combined. Fold in about 1 cup of the toasted pecans and half of the chocolate chips.
Assembly: Scatter the remaining pecans and chocolate chips evenly over the hot crust. Pour the filling over the top and gently tap the pan to remove air bubbles.
Bake at 325°F (reduce the oven temperature) for 28–34 minutes, until the edges are set and the center has a slight wobble. If the top darkens too quickly, tent loosely with foil for the last 10 minutes. Sprinkle with flaky sea salt during the last minute of baking so it lightly adheres.
Cool on a rack for 1 hour, then refrigerate at least 2 hours to set. Lift out using the parchment, slice into 16 bars with a warm knife, and serve.
Practical tip: If your corn syrup is very thick or cold, warm it briefly in the microwave (10–15 seconds) so it blends smoothly without overmixing the eggs.