Grease a 6 x 3-inch springform or removable-bottom cheesecake pan and line the base with parchment. Stir together gingersnap crumbs, 2 teaspoons sugar, citrus zest, and melted butter. Press firmly across the base and about 1 inch up the sides. Freeze while preparing the filling.
Beat the softened cream cheese, 1/2 cup sugar, pumpkin puree, flour, vanilla, cinnamon, nutmeg, ginger, and cloves on low speed until smooth. Scrape the bowl. Mix in the cream and 1/4 cup chopped pecans. Add the eggs and yolk last; mix on low just until blended.
Pour into the crust, leaving at least 1/2 inch of headroom. Cover the pan snugly with foil. Add 1 1/2 cups cold water to a 6-quart Instant Pot, or the minimum required by your model. Set a trivet inside and lower the pan onto it with a heat-safe sling. The pan must sit above the water.
Seal the cooker and select Pressure Cook, High, for 30 minutes. Let the pressure release naturally until the float valve drops; do not force the lid open. The pressure-building and release time is additional to the 30-minute setting.
Carefully lift out the pan and remove the foil without dripping condensation onto the cake. The edges should be set and the center should wobble gently rather than ripple like liquid. Check that the center reaches 160°F with an instant-read thermometer. If below that temperature or still liquid, re-cover, return to the trivet, check that the cooker still has its required water, and pressure-cook 5 minutes more, followed by natural release. Recheck and repeat if needed.
Cool on a rack for about 30 minutes. Run a thin knife around the edge, cover, and refrigerate within 2 hours of cooking. Chill at least 4 hours, preferably overnight, before unmolding. Add the caramel and 1/4 cup topping pecans just before serving. Refrigerate leftovers at 40°F or below and use within 4 days.
