Preheat the oven to 375°F. Line a 12-cup muffin pan with cupcake liners.
Whisk together flour, cocoa powder, salt, baking powder, baking soda, and sugar; set aside.
Mix together egg, cooled butter, vanilla, milk, and sour cream in a large mixing bowl until well combined.
Stir the dry ingredients into the wet ingredients just until combined.
Add ½ cup chocolate chips and fold gently into the batter.
Spoon about 2 tablespoons of batter into the bottom of each muffin liner in the muffin tin. Place one dark chocolate truffle into the center of each muffin cavity and then cover with another scoop of batter.
Sprinkle some additional chocolate chips over the top of the batter, if desired.
Bake for approximately 18 minutes until the tops of the muffins are slightly puffed and appear dry on the top.
Cool muffins for about 10 minutes and then transfer to a cooling rack to finish cooling.
Truffle centers will remain soft and melty while muffins are warm. You can reheat muffins in the microwave for 10-15 seconds to remelt the truffle center.
Reheat leftover ganache in the microwave until fluid. Scoop into a piping bag or a small plastic bag and snip the corner off. Drizzle the ganache over the tops of the muffins.
Melt white chocolate chips in a small microwave-safe bowl. Heat for 30 seconds at a time, stirring until chocolate is fully melted. Drizzle white chocolate over the muffins as well, if you wish.