Heat the oven to 350 F and line baking sheets with parchment paper.
In a medium saucepan over low heat, melt the butter and chopped dark chocolate, stirring until smooth and glossy. Remove from heat.
While the mixture is still warm, whisk in the chipotle chili powder and cinnamon to bloom the spices in the fat. Let sit 1 to 2 minutes.
Whisk the brown sugar into the warm chocolate mixture until thick and glossy. Whisk in the eggs, one at a time, then stir in the vanilla and orange zest, if using.
In a separate bowl, whisk together the flour, masa harina, cocoa powder, allspice, and fine sea salt.
Add the dry ingredients to the chocolate mixture and fold gently just until no dry streaks remain. The dough will be soft and thick, similar to a brownie batter.
Cover the bowl and chill the dough for 45 to 60 minutes, until firm enough to scoop and roll without being overly sticky.
For the coating, combine the granulated sugar, cinnamon for coating, chipotle for coating, and a pinch of salt in a shallow bowl. Place powdered sugar for dusting, if using, in a separate bowl.
Scoop the chilled dough into 1 tablespoon portions and roll into balls. Roll each ball in the chipotle cinnamon sugar coating to cover, then roll lightly in powdered sugar.
Arrange the coated dough balls on the prepared baking sheets, leaving space between them. If using, sprinkle a tiny pinch of smoked salt on top of each ball.
Bake at 350 F for 9 to 11 minutes, rotating sheets once, until the tops are crackled, the edges are just set, and the centers still look soft but not wet. The cookies will firm as they cool.
Cool on the baking sheet for 5 minutes, then transfer the cookies to a rack to cool completely. Store covered at room temperature. The spice flavors deepen by the next day.