Place the gluten-free pie crust in the freezer—this keeps it from shrinking during baking and helps it stay structurally sound. While the crust chills, preheat your oven to 350°F and position a rack in the lower third of the oven, which ensures the bottom crust bakes through without the filling burning.
Melt the butter over low heat or in the microwave, then set it aside to cool to room temperature—this prevents the eggs from scrambling when you mix them in. While the butter cools, crack the eggs into a small bowl and whisk them together with the vanilla extract and bourbon until well combined.
In a large mixing bowl, whisk together the sugar, brown sugar, gluten-free flour, and salt. I recommend pressing the brown sugar firmly with the back of a spoon as you add it to ensure you capture all that deep molasses flavor—it really makes a difference in the final richness. This dry mixture creates the foundation for an evenly textured filling.
Pour the cooled melted butter and the egg mixture from Step 2 into the dry ingredients from Step 3, stirring until just combined—don't overmix, as this keeps the texture tender. Gently fold in the walnuts, pecans, and chocolate chips, distributing them evenly throughout the batter. I like to reserve a small handful of chocolate chips and nuts to sprinkle on top before baking for a more appealing presentation.
Remove the pie crust from the freezer and place it on a baking sheet (this catches any drips and makes handling easier). Pour the filling from Step 4 into the cold crust, smoothing the top gently. Bake for 45-50 minutes, until the filling is set around the edges but the center still has a slight jiggle—it will continue to set as it cools.
Remove the pie from the oven and let it cool on the baking sheet for at least 30 minutes, then transfer it to a wire rack to cool completely. The pie will firm up significantly as it cools, making it much easier to slice cleanly—resist the urge to cut into it while warm, as the filling will be too soft and will fall apart.