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Preheat the oven to 325°F (160°C). Line a 12-cup muffin pan with paper liners.
Combine gluten-free graham cracker crumbs, melted butter, and sugar in a small bowl. Mix until moistened, then press about 1 tablespoon into the bottom of each cupcake liner.
Bake for 5 minutes, then set aside to cool.
In a large bowl, beat the softened cream cheese and sugar until smooth and creamy.
Add eggs one at a time, mixing on low speed after each addition until just combined.
Mix in sour cream, vanilla extract, and vanilla bean paste. Avoid overmixing to keep the texture silky.
Divide the batter evenly among the cupcake liners, filling each about three-quarters full.
Bake for 18–20 minutes, or until centers are just set with a slight jiggle.
Turn off the oven, crack the door slightly, and let the cheesecakes cool for 10 minutes.
Transfer to a wire rack to cool completely before refrigerating for at least 2 hours (or overnight).
Once chilled, remove liners if desired. Sprinkle about 1 teaspoon of sugar evenly over each cheesecake.
Using a kitchen torch, melt the sugar until it turns golden and glassy. Allow to set for a few minutes before serving.