In a large, heavy-bottomed saucepan, combine the whole milk, granulated sugar, and the scraped vanilla bean seeds along with the empty pod.

Place the saucepan over medium heat and stir constantly with a wooden spoon or heatproof spatula until the sugar is completely dissolved, which should take about 5 minutes.

Once the mixture comes to a gentle simmer, carefully stir in the baking soda. The mixture will foam up significantly, which is a normal reaction that helps prevent the milk proteins from coagulating.

Reduce the heat to medium-low to maintain a gentle, steady simmer. Cook uncovered, stirring occasionally, for 45 to 50 minutes as the milk slowly reduces and turns a light golden color.

When the mixture begins to thicken and darkens to a deep, rich caramel brown, stir continuously for the final 5 to 10 minutes to prevent the bottom from scorching.

Remove the saucepan from the heat once the dulce de leche coats the back of a spoon and leaves a clear path when you run your finger through it. Carefully extract the vanilla bean pod, stir in the flaky sea salt, and let it cool completely before transferring to a glass jar; it will continue to thicken as it rests.