Preheat oven to 350 degree. Grease a full-size 12-cup muffin tin.
To make the cream cheese filling, cream together the cream cheese, 1/3 cup sugar and 1/8 teaspoon salt until smooth in a standing mixer with a paddle attachment or by hand with a wooden spoon.
Add the egg and continue to cream until light in color and as thick as sour cream. Fold in chocolate chips and set aside.
To make the batter, combine the rice flour, tapioca starch, soy flour, 1 cup plus 1 teaspoon sugar, coca powder, baking soda and ½ teaspoon salt in a mixing bowl.
Create a well in the dry ingredients and pour in the water, oil, vinegar and vanilla. Mix until smooth.
To fill the muffin tins, put one tablespoon batter into the bottom of each cup. Add a scoop of cream cheese filling on top of the batter, dividing the filling evenly. Distribute the rest of the chocolate batter on top. Muffin cups should be almost, but not completely, full.
Bake in preheated oven for 25 minutes or until cupcakes hold their shape. Cool in the muffin tins for about 20 minutes before turning out and cooling on racks.