Position oven rack in center; preheat to 350°F. Coat a 9-by-13-inch broiler-safe baking dish with cooking spray. Bring a large pot of water to a boil over high heat. Cook 12 ounces of pasta according to package directions. Drain well in a colander; spread on a large rimmed baking sheet. Wipe the pot clean.

Meanwhile, whisk cream cheese pieces, ¾ cup Parmesan, 2 tablespoons nutritional yeast (if using), ¼ teaspoons red pepper flakes, 1 teaspoon lemon zest, ½ teaspoon salt, and ¼ teaspoon nutmeg in a medium bowl until combined. Gradually whisk in 2 cups half-and-half.

Heat 1 tablespoon oil in the pot over medium-high heat. Add minced shallot and minced garlic; cook, stirring constantly, until softened and fragrant, about 1 minute. Gradually add 2 packages spinach; cook, tossing constantly using tongs, until completely wilted, 3 to 5 minutes. Add 2 tablespoons of flour; cook, stirring constantly, until the spinach is evenly coated, about 1 minute. Remove from heat.

Add the cooked pasta, the cream cheese mixture, and ½ cup mozzarella to the pot; stir to combine. Transfer to the prepared baking dish, spreading into an even layer; sprinkle with the remaining ½ cup mozzarella. Cover the dish tightly with foil. Bake until warmed through and slightly bubbling around the edges, 15 to 20 minutes. Remove from oven.

Increase oven temperature to broil. Uncover the baking dish; broil on the center rack until browned on top, about 5 minutes. Garnish with parsley, if desired.