Put a large piece of aluminum foil on a baking sheet; arrange the fish fillets side by side on the foil and sprinkle with 1/2 teaspoon salt.
Combine the achiote paste, lime juice, orange juice, oregano, cumin, scallions, chile powder, vinegar and brown sugar in a blender; pulse until smooth. Pour the mixture over the fish and turn to coat using tongs. Scatter the thyme sprigs and bay leaves over the fish, then top with orange slices. Cover the fish with another piece of foil and crimp the edges to tightly seal. Marinate in the refrigerator, 1 to 4 hours.
Position a rack in the upper third of the oven and preheat to 475 degrees F. Transfer the fish to the oven and bake until tender, about 25 minutes. Remove the herbs and orange slices. Serve the fish in tortillas with assorted toppings.
Charred Spring Onions
Trim 2 bunches spring onions; halve lengthwise, if large. Cook in a large cast-iron skillet over medium-high heat until tender and blackened, 5 to 8 minutes. Cut into pieces and sprinkle with lime juice and salt.