In a medium bowl, stir together the all-purpose flour, cornstarch, baking soda, and salt. Set aside.
In the bowl of a stand mixer fitted with a paddle attachment, beat the butter and creamy peanut butter on medium speed for 1 to 2 minutes or until light and fluffy. Scrape down the sides and bottom of the bowl with a plastic spatula.
Add the light brown sugar and granulated sugar and beat again until combined.
While the mixer is on low speed, add the egg, egg yolk, and vanilla extract. Be sure that each egg gets fully incorporated before adding the next.
Scrape down the sides of the bowl and remove the paddle attachment. This will ensure that all your ingredients are getting incorporated evenly and completely.
Slowly add the flour mixture to the wet ingredients while the mixer is on low. Mix just until all the flour has been incorporated.
Lastly, add the peanut butter baking chips to the dough and stir just until evenly distributed.
Using a large cookie scoop (I used a 2-inch scoop that holds approximately 3 tablespoons of dough), scoop out a dough ball into the palm of your hand. Flatten the dough to an approximately 3-inch circle, place 6 to 7 mini marshmallows into the center of the flattened disc of cookie dough, then fold the sides over the mini marshmallows. You want to enclose all the marshmallows inside the center of the peanut butter cookie dough ball.
Place the mini marshmallow-filled cookie dough ball onto a parchment-lined baking tray and repeat until all the fluffernutter cookies have been formed.
Freeze the tray of cookie dough balls for 1 to 2 hours.
Preheat the oven to 350°F. Line a large baking sheet with parchment paper or a silicone baking mat.
Place 5 to 6 frozen fluffernutter cookie dough balls onto the prepared baking sheet. Bake for 11 to 13 minutes.
Allow the cookies to cool completely on the baking tray before transferring them to a cooling rack while you bake the remaining fluffernutter cookies.