Place the chopped dark chocolate in a heatproof bowl and melt it over a simmering water bath, stirring gently until smooth and glossy. This will create your chocolate shell.
Line your mini muffin tin or silicone molds with paper cups or liners. Spoon a small amount of melted chocolate into each, tilting the mold to coat the sides evenly. Chill in the fridge for about 10 minutes until set.
While the chocolate is chilling, stir together the peanut butter, honey, a pinch of sea salt, and 1 tablespoon of coconut oil until smooth and creamy. If your peanut butter is thick, warm it slightly or thin with a little more coconut oil for better spreading.
Remove the molds from the fridge once the chocolate shells are firm. Drop a small spoonful of peanut butter mixture into the center of each shell, pressing gently to fill the cavity without overflowing.
Warm the Nutella briefly to loosen it, then toast it in a dry skillet until fragrant and slightly darker in color. Let it cool slightly, then spoon a thin layer of toasted Nutella over the peanut butter layer in each mold.
Pour the remaining melted chocolate over each filled mold, sealing the Nutella layer completely. Use a spatula to smooth the top if needed, and sprinkle a tiny pinch of flaky sea salt on each for contrast.
Refrigerate the assembled peanut butter cups for at least 30 minutes until the chocolate is fully set and glossy. Once firm, gently remove them from the molds by peeling away the liners or pushing from the bottom.
Let the peanut butter cups sit at room temperature for 5 minutes before serving. Enjoy the rich, glossy chocolate shell with the creamy, toasted Nutella layer inside for a perfect homemade treat.