1.In a small saucepan, whisk together the rice flour, 3 tablespoons sugar and pinch of salt. Then whisk in the water until smooth. Set the saucepan over medium-low heat and cook, stirring constantly with a stiff rubber spatula, until the mixture is very thick and pulls away from the sides of the pan, about 5 minutes.
2.Dust a clean work surface with potato starch. Transfer the mochi to the prepared surface and use the spatula or your hands to flatten to about 1/2 inch thick. Dust the top with more potato starch and let cool completely, about 20 minutes. Dust any excess potato starch off the cooled mochi and cut into 9 equal-sized pieces.
3.In a medium mixing bowl, whisk together the flour, baking soda and 1 teaspoon salt. Set aside. In a large mixing bowl, add the melted butter, brown sugar and 3/4 cup sugar. Whisk to combine.
4.Add the eggs, one at a time, whisking to incorporate after each addition. Add the vanilla and whisk to incorporate. Add the flour mixture. Using a stiff rubber spatula, fold in the dry ingredients until just combined and smooth.
5.Place oven racks in the upper third and lower third positions. Preheat the oven to 350 degrees F. Line two baking sheets with parchment paper and set aside.
6.Fold in all but 2 tablespoons of the chocolate chunks into the dough. Scoop out a 1/3 cup of the dough using a 1/3-cup ice cream scoop and using your thumb press an indentation in the middle of the cookie dough. Add a piece of the mochi in the middle and then completely enclose the mochi with the cookie dough.
7.Place onto one of the prepared baking sheets. Repeat with the remaining cookie dough and mochi. Press some of the remaining 2 tablespoons of chocolate chunks into the tops of the cookie dough. Sprinkle with flaky salt.
8.Bake in the oven, rotating the pans from top to bottom and front to back after 8 minutes. Continue to bake for another 5 to 7 minutes, or longer if you prefer a darker cookie, until the edges are golden brown and the middle of the cookies are just soft.
9.Cool on the baking sheets for 5 minutes, then remove to cooling racks. Serve warm, if possible. The cookies will keep for 2 to 3 days, well wrapped at room temperature.