Heat-treat the all-purpose flour by microwaving in 30-second intervals, stirring in between, until it reaches an internal temperature of 160 degrees Fahrenheit.
In a medium bowl, whisk together the melted butter, cocoa powder, granulated sugar, and vanilla extract until smooth.
Fold in the graham cracker crumbs until a thick, uniform dough forms.
Press the brownie mixture firmly into the bottom of an 8x8 inch square pan lined with parchment paper.
In a separate large bowl, cream together the softened butter and brown sugar until light and fluffy.
Beat in the milk, vanilla extract, and salt until well incorporated.
Add the heat-treated flour and mix until a cohesive dough forms, then fold in the mini chocolate chips.
Spread the cookie dough layer evenly over the brownie base, smoothing the top with an offset spatula.
Melt the 1/2 cup chocolate chips and coconut oil in the microwave in 20-second intervals until fully liquid.
Pour the chocolate glaze over the cookie dough layer and tilt the pan to coat evenly.
Refrigerate for at least 2 hours to allow all layers to set before slicing into 16 squares.