Position a rack in the center of the oven and heat to 325°F. Lightly grease an 8-inch square pan with spray or butter, then dust the bottom and sides with cocoa powder; tap out any excess.
Microwave the buttermilk just until warm to the touch (10–15 seconds). Stir in the instant coffee and vanilla until dissolved; set aside.
In a large bowl, briskly whisk the eggs, oil, maple syrup, and sea salt until glossy and well emulsified, about 30 seconds.
Whisk the warm coffee–vanilla buttermilk into the egg mixture until smooth.
Sprinkle the brownie mix over the wet ingredients and fold with a spatula just until no dry pockets remain. Fold in 3/4 cup of the chocolate chips. Let the batter rest for 5 minutes to hydrate.
Scrape the batter into the prepared pan and smooth the top. Scatter the remaining 1/4 cup chips over the surface.
Bake until the edges are set, the center has a slight jiggle, and a toothpick inserted 2 inches from the edge comes out with moist crumbs, 43–48 minutes. Rotate the pan once halfway through baking.
Cool the pan on a rack for 20 minutes, then finish with a light sprinkle of flaky sea salt. Cool an additional 15–30 minutes before slicing with a sharp knife, wiping the blade between cuts.