Preheat the oven to 350 degrees. Coat cupcake tins with cooking spray.
Separate the eggs into large bowls; one for egg yolks and one for egg whites. In a small saucepan, melt the baking chocolate and dark chocolate over low heat.
Meanwhile, beat the egg yolks using an electric mixer on medium-high speed until thick, about 7 minutes. Reduce the speed to low, add the sea salt and sugar and mix until the mixture becomes thick and creamy, about 8 minutes. Add the melted chocolate and pistachios and continue to beat with the mixer on low speed.
Add the almond extract to the large bowl of egg whites. Beat until foamy, approximately 3 minutes. Add ¼ cup of the sugar and beat on high speed until soft peaks form, about 5 minutes.
Fold the egg whites into the chocolate mixture. Divide the batter evenly among the cupcake tins. Transfer to the oven and bake until a toothpick inserted in the center of each cupcake comes out clean, about 15-20 minutes.
Remove from the oven and set aside to cool on baking racks. Slice each cupcake in half. Serve warm with a spread of almond butter for a healthy spin on sugary icing.