Whisk flour, salt, and sugar. Cut in butter until crumbs form. Add ice water until dough holds. Chill for 30 minutes.
Toss apples with sugar, flour, cinnamon, nutmeg, lemon juice, and vanilla.
Preheat oven to 375°F; grease a 12-cup muffin tin.
Roll out dough to 1/8-inch thickness; cut 12 (3.5-inch) circles. Press into muffin cups.
Spoon apple filling into crust cups, filling to the top.
Bake for 20-25 minutes until golden. Cool in tin for 10 minutes; transfer to a rack.
Drizzle with caramel sauce and sea salt. Garnish with pecans, powdered sugar, and extra caramel. Serve warm or at room temperature.