Preheat oven to 350°F. Line an 8-inch square pan with parchment, leaving overhang. Lightly coat with spray.
Heat-treat the cookie dough flour: spread 1 1/4 cups flour on a sheet pan and bake 5–7 minutes until it reaches 165°F. Cool completely.
Whisk melted butter and granulated sugar until glossy. Beat in eggs and 1 tsp vanilla until smooth.
Sift in cocoa, flour, and salt. Fold just until no dry spots remain, then stir in chocolate chips.
Spread batter in the pan. Bake 25–30 minutes, until a toothpick comes out with moist crumbs. Cool in pan completely.
Beat softened butter, brown sugar, and granulated sugar until fluffy. Mix in 1 tsp vanilla and 2 tbsp milk.
Add cooled heat-treated flour and salt. Mix until a soft dough forms, adding up to 1 tbsp more milk if needed. Fold in mini chips.
Spread cookie dough evenly over cooled brownies. Chill 20 minutes to firm.
Warm cream until steaming but not boiling. Pour over chocolate chips, let sit 2 minutes, then stir smooth with a pinch of salt.
Pour ganache over the cookie dough. Smooth the top and chill 30–45 minutes until set.
Lift from the pan using the parchment. Slice with a warm knife, wiping between cuts.