Set a rack in the center and preheat the oven to 350 F. Line 2 muffin tins with muffin or cupcake liners.
In a medium bowl, whisk together the rice flour, cornstarch, baking powder, baking soda, spices and salt. In another bowl, whisk together the sugars, vegetable oil and eggs. Make a well in the center of the dry ingredients and whisk in the egg mixture. Whisk until smooth then add in the pumpkin puree also until smooth.
For the filling, beat the cream cheese and sugar until smooth. Add in the egg until smooth, then stir in the chocolate, if using.
Divide the cupcake batter evenly among the prepared muffin cups. Spoon a few tablespoons of the cream cheese filling into the center of each cupcake. Bake for about 20 to 25 minutes, until a toothpick inserted into the chocolate part of the cupcake comes out clean.
* If you are not on a gluten free diet, substitute 1 1/2 cups total all-purpose flour and omit the rice flour and the cornstarch.