In a bowl whisk together the all-purpose flour, whole wheat flour, buckwheat flour, baking powder, and baking soda. In a large mixing bowl beat butter, sugars, and salt with an electric mixer on medium speed for 5 minutes, scraping bowl a couple of times. Add egg and beat 1 minute; add the yolk and beat 1 minute more. Add the dry ingredients all at once and beat on low speed until almost all of the dry ingredients are combined. Add the kasha and beat a few seconds. Add the chocolate and beat on low just until all is combined. Shape into a ball; wrap in plastic wrap. Chill at least 1 hour.
Center rack in oven and preheat to 375 degrees F. Line a baking sheet with parchment paper. Using a medium cookie scoop, scoop level portions of the dough (or rounded tablespoonfuls) and place 2 inches apart on the prepared baking sheet. Sprinkle evenly with flaky salt.
Bake for 8 to 9 minutes (rotate pan front to back after 4 minutes) or just until the edges of the cookies start to brown. (The cookies should look underbaked.) Let cool on baking sheet for 2 minutes. Transfer cookies to a wire rack to cool. The cookies will firm as they cool. Repeat with remaining cookie dough.