In a medium bowl, whisk to combine flour, baking soda, baking powder and salt. Set aside.
In the bowl of a mixer fitted with a paddle attachment, cream butter and sugars together until light and fluffy, about 5 minutes. Add egg and vanilla and mix to combine, scraping down bowl if needed. Add dry ingredients and slowly mix until just combined. Slowly mix in chocolate.
Scoop dough into roughly ¼ cup portions, roll into balls, and arrange on a parchment paper lined baking sheet. Chill at least 1 hour and up to 72 hours.
Preheat oven to 350°F. Space about 4 chilled dough balls out on a parchment paper-lined baking sheet to allow for spreading. Sprinkle flaky salt on the surface and bake for a total of 20-22 minutes. After 10 minutes, pull the pan out, lift it about 6-inches off the counter and gently bang it against the counter to collapse the cookies. Return pan to oven and repeat the banging every 2 minutes. When ready, the cookies will be golden brown and rippled on the edges, but still quite soft in the center.
Let cool 10 minutes on the sheet pan, then transfer to a cooling rack. Cookies will firm up as they cool.