Make the peanut butter (optional). Preheat the oven to 350℉ and line a baking sheet with parchment paper. Scatter the peanuts onto the baking sheet and toast them in the oven for 20-25 minutes, until golden brown and fragrant.
Allow the nuts to cool slightly, about 5 minutes, then transfer them into the bowl of a food processor fitted with a blade attachment. Make sure that any steam from the nuts can release through the machine's feeding tube, otherwise the condensation can drip into the nut butter and cause it to seize.
Allow the machine to run until a nut butter forms, scraping down the sides every few minutes. It will turn from a crumbly flour to a thick paste and then into nut butter (this could take up to 10 minutes). The longer you process it, the runnier the butter will be.
Once a nut butter forms, allow the mixture to cool completely before using.
Make the peanut butter filling. Place the nut butter into a large bowl with the vanilla, salt, and powdered sugar, then stir to combine. Taste and adjust the powdered sugar as needed, adding more if you prefer a sweeter and thicker filling.
With a measuring spoon, portion the peanut butter into heaping ½ tablespoon rounds. Use your hands to flatten each round into a disk approximately ¼'' thick—they should be slightly smaller than the width of a standard muffin tin, around 1 ¾'' wide.
If the filling is too sticky or runny, add the reserved 1 tablespoon of water, stirring in 1 teaspoon at a time as needed until the desired consistency is reached.
Place the peanut butter disks onto a parchment-lined baking sheet, then set the tray in the freezer as you prepare the chocolate.
Assemble. Line two to three muffin tins with cupcake liners and set aside. In the meantime, melt the chocolate over a bain-marie or in the microwave in 30-second bursts, stirring after each increment.
After it's fully melted and smooth, spoon the chocolate into a piping bag and snip off the end. You could use a spoon instead of a piping bag to portion the chocolate, but it may be messier.
Once the peanut butter filling is firm to the touch, remove the tray from the freezer.
To assemble, pipe about 1 tablespoon of chocolate into a cupcake liner, then press a disk of peanut butter into the cup. Top with more chocolate to coat, around 1 tablespoon, then tap the tray to smooth the tops and eliminate air bubbles. Repeat with the remaining disks of filling.
If desired, top the peanut butter cups with flaky salt once the chocolate begins to harden. Refrigerate the muffin tins until the chocolate has set (about 1 hour), then peel off the cupcake liners and enjoy!
Store any leftover peanut butter cups in the fridge for 2 weeks or in the freezer for up to 3 months.