Bake the potatoes until fork-tender, about 45 minutes.
Meanwhile, combine the salt cod, milk, garlic, thyme and onions in a saucepan. Bring to a slow simmer and cook until the cod flakes, 20 to 30 minutes. Strain the mixture, reserving separately both the milk and the cod/garlic/onion mixture. Remove the thyme and discard.
While the potatoes are still warm, rice them through a food mill. Stir the cod mixture into the riced potatoes. Add the butter, creme fraiche and enough of the reserved milk to make it smooth. Season with salt and pepper.
Transfer to a serving bowl, garnish with the capers, dill, parsley and lemon zest and serve with crostini if desired.