Heat oven to 400°F. Line a 12-cup muffin tin with liners and set 4 more liners aside for a second round, if needed.
Whisk flour, baking soda, and salt in a medium bowl; remove 1 tbsp of this mixture and reserve for the berries.
In a heatproof cup or bowl, whisk cocoa with the very hot coffee until smooth. Whisk in the oil and let stand 2 minutes to bloom and cool slightly.
In a large bowl, combine sugar and orange zest (if using), rubbing with fingers to release oils. Whisk in the eggs until slightly thick and lightened, about 30 seconds. Whisk in the yogurt and vanilla, then whisk in the cocoa–coffee mixture until glossy.
Sprinkle the dry ingredients over the wet and fold gently until a few flour streaks remain. Toss blackberries with the reserved tablespoon of flour, then fold them in along with the chocolate chips just until distributed. Let the batter rest 10 minutes to hydrate.
Divide batter among liners, filling each about 3/4 full. Bake at 400°F for 5 minutes, then (without opening the door) reduce oven to 375°F and bake 10–13 minutes more, until the tops spring back and a tester comes out with a few moist crumbs.
Cool muffins in the pan for 5 minutes, then transfer to a rack to cool until warm. Repeat with remaining batter if needed.