Preheat oven to 375 degrees. In a medium pot, heat oil over medium-high. Add onion and cook until softened, about 6 minutes. Add flour and cook, stirring constantly, 1 minute. Gradually add milk, whisking constantly, and cook until slightly thickened and bubbling, about 3 minutes. Season with salt and pepper and let sauce cool slightly.
In a food processor, combine bun, Parmesan, Italian seasoning, and red-pepper flakes. Process until fine crumbs form. Transfer half the mixture to a large bowl and combine with spinach, tuna, and half the sauce; season with salt and pepper. Fill each shell with 2 heaping tablespoons spinach mixture and place in a 9-by-13-inch baking dish. Top with remaining sauce and breadcrumb mixture. Bake until sauce is bubbling and breadcrumbs are golden, about 20 minutes.