Position a rack in the center of the oven and preheat the oven to 350 degrees F. Line two half sheet pans with parchment paper.
In a small bowl, whisk together the flour, baking powder, baking soda, and salt.
In a large bowl, whisk together the coconut oil, almond butter, water, and vanilla until smooth. Add the sugar and whisk until combined. Add the dry ingredients and mix with a rubber spatula until just combined. add the chopped chocolate and mix until evenly distributed throughout.
Use a 3-tablespoon cookie dough scoops to portion the cookie dough into balls and place them at least 3 inches apart on the prepared sheet pans. If the cookie dough seems too soft to scoop, refrigerate for about 45 minutes to an hour. Bake one pan at time for 12 minutes, until the edges have set but the centers are still gooey.
The cookies will look puffed when you pull them out of the oven, but will fall and crack into the perfect cookies as they cool. Cool the cookies on the pan on a wire rack for 20 minutes, or until the edges and bottoms of the cookies feel firm to the touch. Repeat with remaining cookie dough balls (or freeze it to bake later). Serve warm or at room temperature. Top with flaky salt, if you like. The cookies can be stored, in an airtight container at room temperature, for up to 3 days.