Preheat oven to 175°C (350°F). Line a standard size muffin tin with cupcake liners. Melt the chocolate and butter by placing in a large heatproof bowl or a double boiler, and setting over a pan of simmering water. Stir occasionally just until melted, it takes about 5 minutes. Remove bowl from heat. Whisk in sugar and salt until mixture is smooth; whisk in eggs to combine. Gently whisk in flour and cocoa, just until smooth (do not overmix). Spoon 1 heaping tablespoon of batter into each cup. Place 1 peanut butter cup on top, gently pressing into the batter. Top with 2 more tablespoons of batter, covering the peanut butter cup completely. Bake for about 35 minutes, rotating halfway through, and until a cake tester inserted halfway in centers (above peanut butter cup) comes out with a few moist crumbs attached. Cool on wire rack. Cupcakes can be stored up to 3 days in an airtight container at room temperature.