Sweat the shallot. Heat 2 Tbsp olive oil in a skillet over medium heat until soft and translucent, about 2-3 minutes. Season with ½ tsp Kosher salt, then add chopped garlic and ¼ tsp red pepper flakes, then cook 1 minute more.
Cook the spinach. Add fresh spinach to the pan, season with ½ tsp Kosher salt, then cook until wilted, about 2 minutes. Remove from the heat, then add ½ cup sliced basil leaves and 2 Tbsp chopped fresh oregano. Allow to cool slightly.
Make the ricotta cheese mixture. In a large bowl, combine 24oz ricotta cheese, ¾ cup grated Parmesan, 1 egg yolk, 1 tsp fresh lemon zest, ½ tsp black pepper, and ¼ tsp grated nutmeg. Stir until well mixed. Add the cooled spinach mixture, then stir again until thoroughly mixed.
Boil the cannelloni shells. Bring a large pot of salted water to a rapid boil. Blanch the pasta tubes until al dente according to package instructions, then drain. It can be helpful to toss the cooked pasta with a little olive oil to prevent sticking while you fill them.
Stuff the pasta tubes. Place filling in a large Ziploc bag, then cut off the corner and pipe the filling into the pasta tubes. You can also use a spoon to stuff the pasta, if preferred.
Assemble. Spoon 2 cups of marinara sauce along the bottom of a 9x13 baking dish. Place stuffed cannelloni on top in a single layer.
Make the béchamel. Preheat an oven 350°F/175°C. Melt 4 Tbsp unsalted butter over medium heat in a saucepan. When melted, add 2 Tbsp all-purpose flour, then whisk until the flour is a light golden brown, about 3 minutes. You don’t want the flour getting too dark. Quickly whisk in 2-3 cups of warm milk, then increase the heat to medium-high. Bring to a simmer, then continue to cook and whisk for another 3 minutes. Reduce the heat to low, add smashed garlic cloves, then cook until thick, velvety, and smooth, about 8-10 minutes. Stir in ¼ cup grated Parm, ⅛ tsp grated nutmeg, a pinch of cayenne, ½ tsp Kosher salt, and freshly cracked black pepper, to taste.
Bake the cannelloni. Discard the garlic cloves, then pour the béchamel on top of the pasta. If not baking immediately, cover tightly, then refrigerate until needed. Otherwise, bake for 35 minutes.
Broil, then serve. Carefully transfer the dish under a broiler set to high for 1-2 minutes total, just to crisp the edges and brown the top of the pasta. Allow to rest for 10 minutes before serving with additional grated Parmesan and fresh basil leaves.