For the brownies: Preheat the oven to 350 degrees F. Grease a 9-by-13-inch glass baking pan with coconut oil and set aside.
Combine the brownie mix with the eggs, oil and 1/4 cup water in a large bowl. Stir together using a rubber spatula until fully incorporated. Spread in the prepared pan.
For the topping: Combine the almond butter, powdered sugar and coconut oil in a separate bowl. Spoon dollops of this mixture over the top of the brownie batter. Using a toothpick, swirl the two together. Bake until the edges are set and a toothpick inserted an inch from the edge of the pan comes out clean, 25 to 30 minutes. Immediately sprinkle with the flaky salt. Cool completely in the pan before cutting into squares and serving.