Preheat oven to box temperature and line a 12-cup muffin tin; spray lightly if not using liners.
Make brownie batter per box directions; stir in vanilla and a pinch of salt if using.
Fill cups halfway with batter, press 1 tsp chocolate chips or truffle filling into center, then top with more batter until cups are 3/4 full.
Bake 16–20 minutes until edges are set but centers still soft; do not fully harden.
While cupcakes bake, heat cream until steaming and pour over chopped chocolate; stir until smooth to make ganache.
When cupcakes are cool enough to handle, poke a small hole and spoon warm ganache into centers, or pour ganache over tops for extra goo.