Preheat the oven to 350°F. Line a standard muffin pan with paper baking cups.
Make the filling: In the bowl of a stand mixer fitted with a paddle attachment, or using a hand mixer, beat the cold cream cheese and sugar on medium-high speed until fully combined and smooth, about 2 minutes. Add the egg and salt and beat again until well-combined, about 2 more minutes. Fold in the mini chocolate chips with a rubber spatula. Set aside.
Make the batter: In a large bowl, whisk together the gluten-free flour, sugar, baking soda, cocoa powder, espresso powder (if using) and salt.
Add the oil, vinegar, vanilla and hot water. Mix on medium speed for 2–3 minutes, scraping the sides and bottom halfway through, until smooth and fully incorporated. The batter will be thin.
Using a kitchen scoop or large spoon, divide the batter evenly among the prepared liners, filling each about halfway. Dollop about 1½ tablespoons of the cream cheese filling into the center of each.
Bake for 16–18 minutes, until a toothpick inserted into the chocolate base comes out clean with just a few moist crumbs. The cream cheese should look pale on top — pull them the moment it starts to take on any color.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.