Line two cookie sheets with parchment paper.
Combine the all purpose flour, rye flour, baking soda and salt in a medium bowl and whisk to combine.
Combine both sugars in the bowl of a stand mixer fitted with the paddle attachment. Pour in the melted butter and beat together on medium-low speed until well combined.
Beat in the vanilla extract and bourbon followed by the egg and the egg yolk, and beat until well combined, about a minute.
Slowly add in the flour mixture and mix on low speed until a few pockets of flour remain.
Remove bowl from the mixer and fold in the chocolate chunks, while also mixing in any remaining flour. Give the bowl a final scrape to make sure everything is well incorporated.
Cover the bowl with plastic wrap and chill the dough for at least 4 hours or overnight.
Preheat the oven to 350F.
Using a medium size, 2 tablespoon ice cream scoop, scoop out the dough onto the cookie sheets leaving 3" between each cookie.
Sprinkle the tops of the dough balls with flaky salt.
Bake for 12-14 minutes or until the edges are lightly brown and the tops look just set. Transfer to cookie sheets to wire racks to cool slightly.