Heat olive oil in a skillet over medium heat until soft and translucent. Season with Kosher salt, then add chopped garlic and red pepper flakes, then cook.
Add fresh spinach to the pan, season with Kosher salt, then cook until wilted. Remove from the heat, then add sliced basil leaves and chopped fresh oregano. Allow to cool slightly.
In a large bowl, combine ricotta cheese, grated Parmesan, egg yolk, fresh lemon zest, black pepper, and grated nutmeg. Stir until well mixed. Add the cooled spinach mixture, then stir again until thoroughly mixed.
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.
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.
Spoon marinara sauce along the bottom of a 9×13 baking dish. Place stuffed cannelloni on top in a single layer.
Preheat an oven. Melt unsalted butter over medium heat in a saucepan. When melted, add all-purpose flour, then whisk until the flour is a light golden brown. Reduce the heat to low, add smashed garlic cloves, then cook until thick, velvety, and smooth. Stir in grated Parm, grated nutmeg.
Discard the garlic cloves, then pour the béchamel on top of the pasta. If not baking immediately, cover tightly, then refrigerate until needed.
Carefully transfer the dish under a broiler set to high, 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.