Line a baking sheet with paper towels and set aside. Place flour in a shallow dish and generously season with salt. Trim fish fillets so they are approximately the same size, dip in flour, and shake off excess flour.
Fill a large, heavy-bottomed, nonreactive frying pan with 1/2 cup of the oil and heat over medium-high heat until shimmering, about 3 minutes. Working in batches, sauté fish until light golden brown, about 1 to 2 minutes per side. Remove to the paper towel–lined baking sheet and sprinkle with salt.
Discard oil, wipe the pan clean with a paper towel, and add remaining 2 tablespoons oil. Place over medium heat and add onions and anchovy. Season with salt and let cook, stirring occasionally, until onions are translucent and tender, about 15 minutes. Add red wine, vinegar, raisins, orange juice, zest, and bay leaf and increase heat to medium high. Let cook, stirring occasionally, until liquid has reduced by 1/2, about 3 to 4 minutes.
Spread 1/3 of the onion mixture on the bottom of a 13-by-9-inch nonreactive baking dish, and set 1/2 of the fish on top, overlapping fillets just slightly. Season with a touch of freshly ground black pepper, then top with another 1/3 of the onion mixture. Top with remaining fish and season with pepper. Top with remaining onion mixture. Cover and refrigerate 12 hours or overnight.
To serve, remove fish from the refrigerator 30 minutes beforehand. Garnish each serving with parsley and pine nuts.
Beverage pairing: Movia Ribolla Gialla, Slovenia. Such an interesting dish—combining raisins, red wine, orange juice, pine nuts, etc—requires a wine of similar uniqueness. Enter Movia, a Slovenian winery just across the border from Italy. The grape Ribolla Gialla is a mainstay of the region and the winemaking at Movia gives it the breadth to become fruity and savory, and nutty and sharp, just like the dish.
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