Preheat the oven to 325°F.
In a food processor, pulse pretzels into a fine, sand-like crumb. Measure out ¾ cup for the crust, and set aside 2–3 tablespoons for garnish.
Add the graham cracker crumbs, brown sugar, and melted butter to the food processor and pulse until combined.
Press the crumb mixture evenly into a 9-inch pie dish using the bottom of a glass or measuring cup. Press firmly and evenly across the bottom and up the sides.
Bake for 15–20 minutes, until lightly golden. Remove and let cool on a wire rack for 30 minutes.
While the crust cools, use a stand mixer with the whisk attachment to beat the egg yolks and lime zest on medium-low for 2–3 minutes, until lightened in color.
Mix in the sweetened condensed milk, then add the lime juice and vanilla extract. Set aside until the crust has fully cooled.
Pour the filling into the cooled crust and bake for 17–20 minutes. The filling will puff slightly and may take on a light golden color — it should still have a little wiggle when done.
Cool at room temp for 1 hour, then refrigerate for at least 4 hours (or overnight).
Right before serving, make the whipped cream: Combine cold heavy cream, a pinch of sea salt, and vanilla in a stand mixer with the whisk attachment. Slowly add in the powdered sugar while mixing on low. Then increase to medium-high and whip until soft peaks form.
Dollop whipped cream around the edges of the pie and top with pretzel crumbs and lime twists. Sprinkle with flaked sea salt if desired.