How to Make It
Preheat oven to 300°F. Cut scallions in half crosswise, separating white and green parts. Wrap green parts in a damp paper towel, and chill until ready to use. Cut white parts of scallions into 2-inch pieces, and place in a large Dutch oven. Cut tops off spring onions, leaving a 3-inch stalk. (Halve the onions lengthwise if large.) Place in Dutch Oven with scallions. Add garlic, shallots, thyme, and bay leaves to Dutch oven. Add red palm oil and just enough neutral oil to cover the vegetables.
Braise, uncovered, in preheated oven until vegetables are tender when pierced with a paring knife, about 1 hour and 30 minutes, gently stirring in garlic scapes during last 10 minutes of cooking. Carefully remove Dutch oven from oven, and let onion mixture cool slightly, about 20 minutes.
While vegetables are cooling, stir together lime zest and juice, ginger, honey, and 2 tablespoons of the braising oil in a small bowl. Season with kosher salt.
Remove bay leaves and thyme from onion mixture, and discard. Using a slotted spoon or spider, gently remove cooked onion mixture from oil. Remove garlic cloves from their skins. Strain remaining oil through a fine wire-mesh strainer, and store oil in an airtight container in refrigerator for another use. Arrange onion mixture on plates, and spoon lime vinaigrette over top. Thinly slice green parts of scallions on an angle, and sprinkle over onion mixture. Sprinkle with mint leaves and flaky salt. Confited onion mixture may be stored, submerged in oil, in refrigerator for up to 1 month.