Preheat oven to 350°F and line an 8-inch square baking pan with parchment paper. For the crust, whisk together flours, salt, cinnamon, and nutmeg in a medium bowl. Combine melted butter, sugar, and vanilla in a medium bowl. Add flour mixture and fold in until incorporated. Use a piece of parchment paper lightly coated with nonstick spray to press dough evenly into bottom of prepared pan. Bake crust for 18 minutes, until golden and set. Transfer to a wire rack to cool completely, and reduce oven temperature to 325°F.
Place chocolate in a double boiler or in a heatproof bowl over a saucepan of gently simmering water. Slowly melt the chocolate, stirring occasionally until glossy and smooth. Set aside to cool to room temperature. Place cream cheese and yogurt in afood processor and process until combined. Add sugar, spices, salt, and egg; process until smooth. Spoon cream cheese mixture over cooled crust and spread evenly. Dollop cooled chocolate by teaspoons over cream cheese layer and swirl together with a toothpick or wooden skewer; gently tap pan once to remove air bubbles.
Bake for 30 minutes or until set. Remove from oven and cool completely on a wire rack; cover and chill in the refrigerator at least 3 hours. Just before cutting, chill in the freezer for 15 minutes. Carefully lift parchment and place bars on a cutting board; use a sharp knife to trim away raised edges, then cut into bars. Store leftover bars in an airtight container in the refrigerator up to 2 days.