Line an 8×8 inch square baking pan with parchment paper. Make sure to leave a little bit of an overhang on the sides so you can easily lift the bars out once they have set. This is a crucial step for getting clean cuts later on.
In a medium bowl, combine the crushed pretzels, the first 1/2 cup of melted butter, and the granulated sugar. Stir until the pretzels are well coated and the mixture looks like wet sand. Press this firmly into the bottom of your prepared pan using the back of a spoon or a flat measuring cup. Place the pan in the refrigerator to chill while you make the filling.
In a heavy-bottomed saucepan over medium heat, melt the remaining 1/2 cup of cubed butter and the brown sugar together. Once melted, stir in the sweetened condensed milk. Bring the mixture to a gentle boil, stirring constantly to prevent burning. Continue to cook for about 3 to 5 minutes until the mixture thickens and turns a light golden brown. Remove from heat and stir in the alcohol-free vanilla extract.
Pour the hot caramel mixture over the chilled pretzel base. Spread it out evenly with a spatula. Return the pan to the refrigerator for at least 30 minutes to allow the caramel layer to firm up before adding the chocolate.
Place the chocolate chips in a microwave-safe bowl. Heat in 30-second intervals, stirring in between, until the chocolate is completely smooth. Pour the melted chocolate over the caramel layer and spread it to the edges. Sprinkle the flaky sea salt over the top while the chocolate is still wet. Chill the bars for at least 2 hours or until completely firm.
