Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
In a small bowl, combine the chopped peaches and 1 tablespoon of honey. Set aside to marinate while you prepare the batter.
In a medium bowl, whisk together the flour, baking powder, baking soda, and salt.
In a large bowl, use an electric mixer to cream butter and 1/2 cup granulated sugar until light and fluffy, about 2-3 minutes.
Add eggs one at a time, beating well after each addition. Mix in 1 teaspoon vanilla extract.
Add the dry ingredients to the butter mixture in three parts, alternating with sour cream and milk. Begin and end with dry ingredients. Mix just until combined.
Gently fold in the peaches and any juices from the bowl using a rubber spatula.
In a separate small bowl, combine cream cheese, 3 tablespoons sugar, and 1 teaspoon vanilla extract for the filling until smooth.
Spoon about 1 tablespoon of cupcake batter into each liner, then add 1 teaspoon of cream cheese filling to the center. Top with another tablespoon of batter to cover.
Bake for 20-22 minutes, or until a toothpick inserted near the edge comes out clean. The centers may remain slightly soft. Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Once cooled, drizzle each cupcake with the remaining honey before serving.