Preheat the oven to 365 (F) -- this is a 40 degree (F) increase from the original sea-level recipe temperature of 325 (F).
Put 1 1/2 cups flour, 1/2 cup plus 1 tablespoon sugar, 1/3 cup cocoa powder, and 1/2 teaspoon baking soda in a large bowl and mix with a handheld electric whisk on slow speed until all the dry ingredients are well incorporated.
Put 1/4 cup sunflower oil, 1 1/2 teaspoons white vinegar, 1/2 teaspoon vanilla extract, and 1 cup water in a glass and whisk to combine.
While the electric whisk is running in the flour bowl, slowly add the oil mixture, increasing the speed of the blender as the mixture thickens. Continue to beat until all the ingredients are incorporated, scraping any unmixed ingredients from the side of the bowl with a rubber spatula.
Spoon 2 tablespoons of the chocolate batter into paper cases and set aside.
Combine 4 1/2 oz. cream cheese, 1/3 cup sugar, 1 egg, 1/2 teaspoon vanilla extract, and a pinch of salt in the bowl of a freestanding electric mixer. Beat together with a paddle attachment (or use a handheld electric whisk) on medium-slow speed until smooth and fluffy.
When the cream cheese batter is fluffy and thick, stir in 2/3 cup chocolate chips with a rubber spatula or a wooden spoon until evenly dispersed. Do not overmix, or the cream cheese will start to split.
Scoop about 1 tablespoon of the cheesecake filing on top of the cupcake batter in the cases and bake in the preheated oven for 22-24 minutes, or until the chocolate part of the cupcakes are smooth and firm to the touch and the cheesecake filing has an even golden color/brown edges. Do not overbake as the cheesecake will become very dry and crumbly.
Let the cupcakes cool slightly in the pan before turning out onto a wire rack to cool completely.
When the cupcakes are cold, spoon the Cream Cheese Frosting (recipe below) on top. Decorate with a light sprinkling of cocoa powder.