Lightly flour a rimmed baking sheet and set it aside.
Place the drained cottage cheese in a food processor and blend until smooth, then transfer to a mixing bowl.
Add the grated Parmesan, egg yolk, kosher salt, black pepper, and nutmeg to the bowl and stir to combine.
Stir in 3/4 cup of the flour with a rubber spatula until the mixture just comes together into a sticky dough; add the remaining 2 tablespoons flour and more flour 1 tablespoon at a time only if the dough will not hold together.
Lightly flour your hands and roll the dough into about 36 rustic, quarter-sized balls, placing them on the prepared baking sheet; re-flour hands as needed.
Chill the baking sheet with the gnudi in the refrigerator for 30 minutes while you heat the sauce and bring a large pot of salted water to a boil.
Warm the marinara sauce over low heat until it simmers, covering the pot; keep warm.
When the water is boiling, gently add the chilled gnudi and cook for 3 to 4 minutes, until they float to the surface.
Use a slotted spoon to transfer the cooked gnudi directly into the pot with the simmering sauce and stir gently to coat.
Divide the gnudi and sauce among four bowls, top with fresh basil and additional Parmesan, and serve immediately.
