Line a baking sheet with wax paper, parchment paper, or a silicone liner. This will give you a flat surface to lay each pretzel bite on.
In a medium bowl, add the ½ cup (1 stick) softened butter, and add ½ cup brown sugar and ¼ cup sugar and cream together.
Add ¼ tsp salt, 1 tsp vanilla, and 2 Tbsp milk and mix together. Add 1¼ cup flour to the mixture and mix until it forms a thick and not sticky cookie dough.
Add ½ cup mini chocolate chips and fold in, stirring gently to evenly distribute the chocolate chips.
Take roughly 1 tsp - 1 Tbsp of cookie dough mixture and roll into balls. Sandwich between two pretzels and remove any excess. Place on the lined baking sheet and repeat for remaining pretzel bites.
Optional: Refrigerate pretzel bites for 30 minutes or freeze for 15 minutes. This will help keep them together when dipping in chocolate.
Add 1 cup chocolate chips to a microwave safe bowl. Microwave in 30 second increments, stirring between each zap. (Optional) If melted chocolate is too thick, add vegetable shortening or coconut oil to taste to thin the chocolate.
Dip each sandwich in the melted chocolate, then set on the baking sheet. Sprinkle with flaky salt if desired.
Allow 30-90 minutes for the chocolate to set. Best served within 24-48 hours. Because of the moisture in the cookie dough, they'll begin to get stale after a day. Store in an airtight container in the fridge.