Pat the fish very dry with paper towels. Season both sides with 1/2 teaspoon of the salt and the black pepper. Spread the flour on a plate and lightly coat each fillet, shaking off the excess.
Heat the oil in a large, heavy skillet over medium to medium-high heat until it shimmers. Carefully add the fish in a single layer; cook in batches if needed. Fry for 3 to 4 minutes per side, depending on thickness, until golden and the fish flakes easily. Transfer to a paper towel-lined plate.
Carefully pour off all but 1 tablespoon of oil from the skillet. Add the onion, carrot, bell pepper, garlic, and whole pierced chile. Cook over medium heat for 2 to 3 minutes, stirring often, until the vegetables begin to soften but still have some crunch.
Add the vinegar, water, sugar, allspice, dried thyme, and remaining 1/4 teaspoon salt. Bring the mixture to a gentle simmer and cook for 3 to 4 minutes, until the sugar dissolves and the vegetables are bright and lightly pickled.
Place the fried fish on a serving platter or individual plates. Spoon the hot pickled vegetables and their tangy liquid over the fish. Serve right away with rice and peas, plain rice, fried plantains, or festival dough.
Check that the thickest portion of the fish reaches 145°F (63°C) on an instant-read thermometer before serving.