Cook the noodles according to the package instructions. Drain, reserving about ½ cup of the pasta water, and set them aside.
Heat the olive oil in a pot over medium heat. Add the tomatoes and a small pinch of salt. Cook, stirring occasionally, until the tomatoes begin to burst, about 5 minutes.
Add the minced garlic and red pepper flakes. Cook until softened and fragrant, about 30 seconds.
Lightly smash the tomatoes with the back of a wooden spoon to help create a sauce. Continue to cook, stirring occasionally, until the sauce has thickened and the tomatoes have mostly broken down, about 10 minutes. Add in a pinch of sugar.
Whisk in the miso paste and about 2 tablespoons of the reserved hot pasta water until smooth. Keep adding more water as needed until the sauce is smooth.
Toss in the drained noodles to coat. Remove from the heat and stir in the Parmesan cheese. Top with more Parmesan, everything but the bagel seasoning, and fresh herbs. Serve.