To make filling: Stir together peanut butter, sugar and a pinch of salt (if using) in a small bowl. Drop by 24 teaspoonfuls onto parchment-lined baking sheet and freeze until solid.
To make cookie dough: Heat chocolate in a double boiler (or a large heat-safe bowl set over a pot of simmering water) until about 90% melted. Remove from heat and stir to finish melting completely. Stir in sugar and salt while still hot, then allow to cool 5 minutes.
Slowly add a couple of tablespoonfuls of the chocolate mixture to the beaten eggs while whisking constantly to temper them (prevent them from curdling). Then gradually stir the egg mixture into the remaining chocolate batter along with vanilla extract.
In a separate bowl, whisk together the flour, cocoa, baking powder and salt. Add to chocolate mixture and stir well to fully incorporate. Refrigerate at least 1 hour (or up to 48 hours).
To make cookies, shape dough into 1 1/2" balls. To stuff them, flatten the ball, place a ball of frozen peanut butter filling in the center, then fold the cookie dough up over it and pinch shut. Roll between palms to form a nice ball again. Top with a few pieces of chopped peanut butter cup and a sprinkle of salt. Repeat with remaining dough.
Place cookies 2" apart on parchment-lined baking sheets (they spread quite a lot and will stick if no parchment!) and freeze for 10 minutes while you preheat the oven to 375ºF (this reduces their spreading).
Bake 8-9 minutes, until crackled at edges and still slightly underdone in centers. Cool a few minutes on baking sheet before transfering to wire cooling racks. Be sure to cool baking sheets (I just run them under cold water - I've never had too much warping occur as a result) between batches as warm sheets will cause the cookies to spread too quickly.