Preheat the oven to 375°F (190°C).
Bring a large pot of salted water to a boil and cook the jumbo shells according to package directions until al dente; drain, rinse with cold water, and set aside to cool.
Heat the olive oil in a large skillet over medium heat and cook the finely chopped onion until softened, about 3–5 minutes; remove from heat and let cool slightly.
Place the cottage cheese in a food processor and purée until smooth, then transfer to a large bowl.
Add the breadcrumbs, nutmeg, and 1/2 cup of the Parmesan to the puréed cottage cheese and mix until combined.
Stir the cooked onions and the well-drained spinach into the cheese mixture, season with salt and pepper, then stir in the lightly beaten egg white until evenly incorporated.
Spoon about 2 tablespoons of the cheese and spinach filling into each cooled shell and place the stuffed shells in a single layer in a 9x13-inch baking dish.
Spread 1 cup of marinara sauce across the bottom of the baking dish, arrange the stuffed shells on top, spoon the remaining marinara over the shells, and sprinkle with the remaining 1/4 cup Parmesan.
Bake uncovered at 375°F for about 30 minutes, until heated through and the top is lightly golden; tent with foil if browning too quickly.
Remove from the oven and let rest 10 minutes before serving.
