Make crust: In a food processor, pulse flour, sugar, and salt. Add butter and pulse until mixture resembles coarse crumbs. Add ice water 1 tablespoon at a time until dough just comes together. Press into a 9-inch tart pan with removable bottom. Chill 15 minutes.
Bake crust: Preheat oven to 350°F. Prick crust with a fork, line with parchment, fill with pie weights, and bake 15 minutes. Remove weights, bake 10 more minutes until golden. Cool completely.
Caramel filling: In a saucepan, combine sugar and water over medium heat. Cook (without stirring) until amber. Remove from heat, whisk in butter and cream carefully (it will bubble). Stir in vanilla, salt, and toasted pecans. Spread evenly in cooled crust. Chill 20 minutes.
Ganache topping: Heat cream until steaming, pour over chocolate chips in a bowl. Let sit 2 minutes, then stir until smooth. Pour over caramel pecan layer, smoothing with spatula.
Finish & serve: Chill tart until set, about 2 hours. Slice and sprinkle with flaky sea salt if desired.