Line a mini muffin pan with 24 liners.
Melt 1 1/4 cups of chocolate chips (microwave in 30-second intervals, stirring until melted). Drop 1 teaspoon of chocolate into each liner. Use the back of a small spoon to brush the chocolate up the sides of the liner, ensuring full coverage. Place in the freezer for 10 minutes.
Once the chocolate is firm, add a teaspoon of creamy peanut butter to each cup. Return to the freezer while you make the pumpkin seed candy.
Heat a large skillet over medium-high heat. Add pepitas and toast, stirring constantly until seeds pop and become slightly golden, about 3 minutes. Transfer to a bowl to cool.
Heat coconut sugar and honey in a saucepan over medium-high heat, stirring to dissolve sugar (about 3 minutes). Add the pepitas and peanuts, cook for 3-4 minutes until temperature reaches 240-285°F. Remove from heat, stir in coconut oil and vanilla extract. Cool for 3-4 minutes until slightly thickened.
Divide the candy mixture among the 24 cups.
Melt the remaining chocolate chips. Cover the candy with chocolate, smoothing with a spoon. Sprinkle with flaky sea salt, if desired.
Place in the fridge until firm, about 20 minutes. Store in the fridge for best results.