Place a rack in middle of oven; preheat to 375°. Mash and stir together 1 Tbsp. cream cheese and ½ tsp. granulated sugar in a small bowl until smooth. Divide cream cheese mixture in half (eyeballing is fine) and roll each piece into a ball. Place on a small plate and chill while you make the dough.

Microwave 1 oz. semisweet or bittersweet chocolate (68%-70% cacao) and 2 Tbsp. unsalted butter in a medium microwave-safe bowl in 20-second bursts, stirring after each burst, until just melted and smooth; be careful not to overheat. (Alternatively, you can melt in a small saucepan over medium-low heat, stirring often.) Let cool 2 minutes.

Add 1 large egg yolk, ½ tsp. vanilla extract, ¼ tsp. Diamond Crystal or Morton kosher salt, ⅛ tsp. baking soda, and remaining ¼ cup (50 g) granulated sugar to chocolate mixture and stir with a rubber spatula until combined and smooth. Add 3 Tbsp. all-purpose flour and 2 Tbsp. Dutch-process cocoa powder and stir just to incorporate (dough may look slightly greasy).

Divide dough in half and shape each piece into a thick patty. Working one at a time, place a cream cheese ball in the center of patties, wrap dough around cream cheese to cover, and seal edges closed. Roll between your palms to smooth into balls.

Place cookies on a parchment-lined baking sheet, spacing 2" apart, and bake until set around the edges and surface is mostly matte, 7-9 minutes. If cookies look very puffy, rap baking sheet sharply on counter. Let cookies cool on baking sheet 5 minutes before serving.