Combine the flour, baking soda, and salt in a medium bowl. Set aside.
In a large mixing bowl, or the bowl of a stand mixer, add both sugars and the cooled, melted butter. Beat until well combined — the mixture will resemble a thick, grainy caramel. Add the egg, egg yolk, honey, and vanilla, and continue beating until incorporated. Then add the peanut butter and beat until smooth.
Gradually add the dry ingredients and mix until just combined.
Fold roughly 2/3 of the chocolate chunks into the cookie dough (reserve the remaining 1/3 for pressing into the tops).
Cover the bowl with cling film and chill for a minimum of 1 hour, ideally overnight (12-24 hours).
Preheat the oven to 180℃ (160℃ fan/350℉) and line 2 baking sheets with parchment paper.
Remove the dough from the fridge. if it's too firm to scoop, allow it to sit at room temperature for 10 minutes to soften up. For medium-sized cookies, scoop about 2-3 tbsp of dough at a time and roll lightly between your palms to form a ball. Arrange 5 cm (2 in) apart on a lined baking sheet. Press a few larger pieces of chocolate into the top and sides of each cookie.
Bake the cookies for 10-11 minutes, or until the edges are just starting to brown. As soon as they come out of the oven, firmly tap the baking sheet once or twice on the countertop. This deflates the cookies, keeping the middles soft and chewy. Allow to cool on the baking sheet for 10 minutes before transferring to a wire rack.