Preheat your oven to 425°F. Grease two baking cups of your cupcake pan. Sprinkle granulated sugar over the entire cupcake cup, sides included, like you're making a souffle.
In a medium bowl, whisk egg. Slowly whisk in cooled chocolate mixture and 1/2 teaspoon of the gel food coloring. Stir in flour and salt.
In a small bowl, whisk together cream cheese, sugar, remaining 1/4 teaspoon food coloring, and vanilla. Transfer mixture to a disposable plastic bag (or piping bag) and snip off one corner.
Divide chocolate mixture evenly between your prepared cupcake cups. Insert piping bag into the center of the batter and divide cream cheese mixture evenly between the cups.