Preheat oven to 350 F. Prepare a cupcake tin with liners.
In the bowl of a stand mixer fitted with the paddle attachment, combine sugar & chili flakes. Mix for a few minutes, until sugar takes on a slight pink hue.
Add soft butter and brown sugar; beat until creamy, 2 minutes. Add eggs, one at a time, scraping down the sides of the bowl with a spatula as necessary.
In a medium bowl, combine flour, cocoa, spices, and soda. Whisk together buttermilk & lime juice in a separate bowl. Add 1/3 flour mix to the stand mixer and stir on low until barely combined. Mix in 1/2 of buttermilk. Continue alternating buttermilk with dry ingredients, ending with the flour mix.
Gradually, with mixer on low, stir in boiling water until just combined.
Pour, pipe, or scoop batter into prepared tins and bake until cakes spring back when touched, about 23-25 minutes.
Allow to cool completely.