Thaw the frozen spinach and squeeze out all excess liquid until almost dry; chop if pieces are large.
In a mixing bowl combine the squeezed spinach, 1½ cups shredded mozzarella, Parmesan, cottage cheese, lightly beaten egg, minced garlic, Italian seasoning, salt, cracked pepper, and crushed red pepper; stir until well combined and set aside.
Bring a large pot of salted water to a boil and cook the jumbo shells until just under al dente (about 1 minute less than package directions); drain, rinse with cool water to stop cooking, toss very lightly with a little olive oil to prevent sticking, and arrange in a single layer on a parchment-lined baking sheet.
While the shells cook, heat a drizzle of olive oil in a large skillet over medium-high heat; add the diced onion and sauté until translucent, about 3–4 minutes.
Add the ground sirloin to the skillet, break into pieces, and cook until no longer pink, about 7–10 minutes; drain excess grease and let the meat cool briefly.
Stir half of the slightly cooled cooked beef (reserve the other half) into the spinach and cheese mixture to make the stuffing.
Preheat the oven to 350°F (175°C). Lightly spray a 9x13-inch baking pan and spread 1½ cups of marinara sauce evenly on the bottom.
Mix the remaining cooked beef and onion into the rest of the marinara to create the topping meat sauce.
Stuff each cooked jumbo shell with about 2½–3 tablespoons of the spinach-cheese-beef filling and place them open-side up in the prepared baking pan in an even layer.
Pour the meat-marinara sauce over the stuffed shells to cover them, then sprinkle the remaining 1½ cups shredded mozzarella evenly over the top and cover the pan with foil.
Bake covered for 25–30 minutes until bubbling, remove the foil, then bake uncovered another 10 minutes until the cheese is melted and lightly golden.
Sprinkle chopped fresh basil over the shells and let rest 5–10 minutes before serving.