Preheat oven to 350°F. Coat a 13- x 9-inch baking pan with baking spray with flour. Bring a medium pot with 1 inch of water to a simmer over low. Set a medium-size heatproof glass bowl over pot. Add chopped bittersweet chocolate and butter to bowl; cook, stirring occasionally, until melted, about 2 minutes. Remove from heat; cool slightly, about 10 minutes.

Whisk eggs, granulated sugar, brown sugar, bourbon, and espresso granules into cooled chocolate-butter mixture until well combined. Stir in flour and kosher salt until combined. Pour half of the batter into prepared pan. Sprinkle with 1 cup of the chopped semisweet chocolate. Top with remaining batter, smoothing with an offset spatula. Sprinkle with remaining 1 cup chopped semisweet chocolate.

Bake in preheated oven until center is set, about 25 minutes. Remove from oven; sprinkle with flaky sea salt. Cool completely in pan, about 1 hour. Slice into 32 bars.