Melt the butter in a large skillet over medium-high heat. Add half of the spinach and cook until wilted, about 2 minutes. Add the remaining spinach, the nutmeg, 1 teaspoon salt and a few grinds of pepper. Cook until all of the spinach wilts, about 3 more minutes. Drain the spinach in a colander and let cool, then squeeze out the excess moisture. Chop the spinach.
Butter a 9-by-13-inch baking dish. Whisk the eggs, milk, lemon zest, 1 teaspoon salt and a few grinds of pepper in a large bowl. Arrange half of the English muffin pieces in the prepared baking dish. Top with half each of the spinach, scallions and cheese. Top with the remaining English muffin pieces, spinach, scallions and cheese. Pour the egg mixture onto the casserole, then press down on the English muffins to submerge them. Cover with foil and refrigerate 3 hours or overnight.
Remove the casserole from the refrigerator 30 minutes before baking. Preheat the oven to 375 degrees F. Bake the casserole, covered, until just set, about 25 minutes. Uncover and bake until the top is lightly browned, about 20 more minutes. Let cool 10 minutes before serving. Serve with creme fraiche.