Melt chocolate chips and coconut oil in a small saucepan over low heat, stirring constantly, until about half of the chocolate chips are melted (~1 minute). Remove the pan from the heat and stir until the chocolate is completely melted. You could also do this in the microwave, melting the chocolate in 30-second increments.
Line a mini muffin pan with 15 mini muffin liners (paper or silicone). If you don’t have a mini muffin pan, you can place the liners on a plate (preferably with a raised edge). Make sure the muffin pan or plate will fit in your freezer before continuing.
Fill the liners with 1 teaspoon of the chocolate mixture. Spread the chocolate in the liners until it's ¾ of the way up the sides. The best way to do this is to pick up the muffin liner and move the chocolate around in the liner until gravity spreads it evenly. Continue until you have 15 chocolate shells (as the original recipe is written). Reserve remaining melted chocolate for the top layer of the peanut butter cups.
Place the muffin pan or plate in the freezer for 5-10 minutes or until the chocolate is firm.
While the chocolate is solidifying, make the peanut butter filling. In a small mixing bowl, combine the peanut butter, almond flour (starting with the lesser amount), powdered coconut sugar, and salt. Stir until smooth, adding more almond flour (1 Tbsp at a time) until the mixture is no longer runny — it should hold its form slightly when scooped on a spoon (see photo). Add more almond flour as needed.
Grab your chilled chocolate shells from the freezer. Place 1 - 1 ½ teaspoons of peanut butter filling into the center of each chocolate shell (a small cookie scoop is helpful here). Tap your muffin tin or plate on the counter a few times to help the peanut butter layer settle and flatten out. Then transfer to the freezer for 10-15 minutes or until firm. If there is any extra filling, it can be reserved for future peanut butter cups or spread onto toast.
Remove from the freezer and place ~¾ tsp of melted chocolate mixture on top of each peanut butter cup (or however much it takes to cover the peanut butter layer and meet the edges of the chocolate sides) and gently shake to completely cover the top. Immediately sprinkle with flaky sea salt (such as Maldon // optional).
Continue with remaining peanut butter cups until all are topped with chocolate. Then place the pan or plate back in the freezer for 5-10 minutes to set.
Remove from the freezer and let the peanut butter cups come to room temperature before enjoying! Store in a sealed container in the fridge for up to 1 week or in the freezer up to 1 month (if you can resist them that long!).