Arrange a rack in center of oven; preheat to 375°. Line a 9" x 9" baking dish with parchment, leaving overhang on 2 opposite sides.

In a food processor, pulse graham crackers until finely ground. Add butter, salt, and 3 Tbsp. sugar and pulse until mixture resembles wet sand and starts to clump together. Firmly press into prepared pan in an even layer, making sure edges are even.

Bake crust until lightly golden and set, about 10 minutes. Transfer to a wire rack and let cool slightly. Reduce oven temperature to 325°.

In the large bowl of a stand mixer fitted with the paddle attachment (or in a large bowl using a handheld mixer), beat cream cheese and remaining ½ cup sugar until smooth and no lumps remain. Add pistachio butter and beat until incorporated and silky. Add eggs, one at a time, beating to blend after each addition and scraping down sides of bowl as needed. Add vanilla and beat until smooth. Pour filling over warm crust and smooth top.

Bake bars until edges are set and center is slightly jiggly, 30 to 35 minutes. Transfer to a wire rack and let cool to room temperature.

Place chocolate chips in a heatproof bowl. In a small saucepan over medium heat, heat cream until just steaming, then pour over chocolate. Let sit 2 to 3 minutes, then stir until smooth and glossy.

Spread ganache evenly over cooled cheesecake. Sprinkle chopped pistachios over while ganache is still soft. Refrigerate until fully set, at least 4 hours and up to overnight.