Preheat the oven to 350°F (180°F). Lightly grease the bottom and sides of an 8-inch (2 L) square baking pan with coconut oil. Cut a length of parchment paper long enough to line the bottom of the pan with extra hanging over the sides.
Make the shortbread base: In a medium bowl, whisk together the almond flour, coconut oil, maple syrup, vanilla, and salt. Evenly press the mixture into the baking pan and lightly prick the base all over with a fork. Bake until the edges start to firm up and turn golden, 13 to 15 minutes. Remove from the oven and let cool for 10 minutes while you prepare the caramel layer.
Make the caramel layer: In a small bowl, whisk together the peanut butter, maple syrup, coconut oil, vanilla, and salt. Spread the caramel mixture over the shortbread base, then place the baking pan in the fridge while you prepare the chocolate layer.
Make the chocolate layer: In a small pot, bring 2 inches (5 cm) of water to a simmer over medium heat. Stir the chocolate chips with the coconut oil in a small heatproof bowl. Set the bowl over the simmering water. Ensure that the bottom of the bowl is not touching the water.
Gently and continuously stir until the chocolate and coconut oil are melted and smooth. Remove from the heat and let sit for a few minutes to thicken slightly. Pour the melted chocolate mixture over the caramel layer. Sprinkle some flaky sea salt over the chocolate, if using. Place the pan in the fridge until firm, about 30 minutes.
Remove from the pan using the parchment paper overhang. Cut into bars. Store in an airtight container in the fridge for up to 1 week.