Lightly spray an 8- by 8-inch baking pan with cooking spray. Line bottom and sides with parchment paper, leaving a 2-inch overhang on 2 sides. Lightly spray parchment with cooking spray; set aside.

In a food processor, pulse cookies until finely ground, stopping to scrape down sides of bowl as needed, about 15 pulses. In a small microwave-safe bowl, microwave 8 tablespoons butter on high, stirring occasionally, until melted, about 1 minute. Stir melted butter, sugar, and ¼ teaspoon salt into ground cookies. Transfer to prepared baking pan. Firmly press crumbs to form a compact, even layer across the bottom of the pan. Freeze, uncovered, until firm, about 15 minutes.

In a large microwave-safe bowl, combine 2 cups chocolate and 4 tablespoons of the butter; microwave on high, stirring every 30 seconds, until melted and smooth, about 2 minutes. Stir in sweetened condensed milk, instant espresso, vanilla, and remaining ½ teaspoon salt. Pour mixture into chilled crust; spread into an even layer. Refrigerate, uncovered, until set, about 1 hour.

In a medium microwave-safe bowl, combine remaining ½ cup chocolate and remaining 4 tablespoons butter. Microwave on high, stirring occasionally, until melted, about 1 minute. Stir until completely combined. Pour over chilled chocolate layer and spread into an even layer. Refrigerate, uncovered, until set, about 30 minutes. Sprinkle with flaky sea salt. Lift parchment to remove bars from pan, and transfer to a cutting board. Cut into 36 squares.