Place 2 Tbsp. jarred caramel topping in bottom of each of 4 (1 1/4-cup) rocks glasses, and sprinkle each with 1/4 tsp. flaky sea salt. Process vanilla ice cream, butter-pecan ice cream, and whole milk in a blender until foamy and thick, 3 to 4 minutes.
Divide milkshake evenly among prepared rocks glasses; top each with 1/4 cup whipped cream, and drizzle each with 1 Tbsp. caramel topping. Sprinkle each with 1/4 tsp. flaky sea salt, and top each with 1 Tbsp. chopped toasted pecans. Serve immediately.