Preheat oven to 350°F (375°F for high altitude).
Combine chopped chocolate, cocoa powder, and hot coffee in a bowl.
Let sit for 1 minute, then whisk until smooth.
Refrigerate mixture for 15–20 minutes until fully cooled.
Whisk in oil, eggs, vinegar, and vanilla.
Add salt and baking soda, whisking until incorporated.
Add sugar and bread flour, whisking until smooth.
Divide batter evenly into 12 lined muffin cups.
Bake for 17–19 minutes (16–18 for high altitude), until a toothpick comes out clean.
Cool cupcakes in the pan for 10 minutes, then transfer to a rack to cool completely.
Meanwhile, heat cream, sugar, and corn syrup in a small saucepan until hot.
Pour hot mixture over semisweet chocolate and let sit for 2 minutes.
Stir until chocolate is melted.
Add butter and stir until smooth and glossy.
Allow frosting to cool 10–20 minutes, stirring occasionally, until thickened.
If too firm, warm briefly for 10 seconds.
Once cupcakes are cooled, core out the center using a corer or knife.
Fill each cupcake with caramel sauce.
Pipe or spread the chocolate frosting on top.
Sprinkle lightly with sea salt before serving.