Preheat your oven to 350F and line two baking sheets with parchment paper or silicone mats.
In the bowl of a stand mixer, put softened butter, brown sugar, granulated sugar, baking powder, baking soda, and salt. Using the paddle attachment, beat until the butter and sugars are creamed. It should be lighter in color and fluffy, similar to frosting. You can also cream the butter and sugars with a handheld electric mixer.
Add egg and vanilla extract and beat again until the mixture is homogenous.
Add the whole wheat flour and kinako and very gently mix until a dough starts to form.
Add the chocolate chips and gently mix again to disperse the chocolate throughout the cookie dough.
Scoop the dough and roll into balls. If using a 2-tbsp cookie scoop, you can get about 24 small cookies. I like to make mine larger, for about 16 cookies.
Place the cookie dough spheres onto your prepared baking sheet, spacing about 2 inches apart. Bake for 10-12 minutes. These cookies are naturally soft in texture due to the combination of flours used.
Immediately after removing the cookies from the oven, sprinkle the flaky sea salt, if using. Leftovers can be kept in an airtight container at room temperature.