In a large bowl, whisk together the melted butter and brown sugar until fully dissolved. Whisk in the vanilla and egg yolks until combined. Add the gluten-free all-purpose flour, almond flour, baking soda, and salt to the bowl. Lightly mix the dry ingredients on top, then fold into the wet ingredients to form the dough.
Once the dough is just combined, gently fold in the chocolate chips. Use a cookie scoop to form 16-18 golf ball size spheres. Place on a parchment-lined baking sheet or in a reusable container. Freeze for approximately 45 minutes to chill the dough.
Just before ready to bake, preheat your oven to 375°F. Prepare 2 large baking sheets with parchment paper. Remove the cookie balls from the freezer and arrange with space between them. Press the tops down slightly. Bake for 12-15 minutes, until the edges are just golden. If you have baking sheets on different racks, switch them halfway through the cook time so everything bakes evenly.
While the cookies are baking, prepare the peanut butter cups. If using regular sized peanut butter cups, cut into 8 mini slices (like you would cut a pizza). If using mini cups, slice in half. Each cookie will need 4 peanut butter cup pieces.
I usually remove the cookies after 13 minutes in the oven. They may not look done but they will firm up as they cool. While they're still hot, grab the baking sheet and slam it a few times. This will help spread the cookies slightly and give them nice crinkles.
Top with 4 peanut butter cup pieces per cookie. Slightly press them into the tops of the warm cookies. For perfectly-shaped cookies, use a large-rimmed glass or cookie cutter and lightly run the edge around the cookies. Sprinkle flakey sea salt on top if you wish.
Cookies should be cooled on the baking sheet for 5 minutes then transferred to a wire rack to cool completely. They can be stored in an air tight container for up to 4 days... if they last that long. Cookie dough could also be kept in the freezer in an air tight container for up to 1 week before being baked. Enjoy!