Preheat the oven to 425F. Prepare a large sheet pan.
Add the zucchini, bell pepper, onion, cherry tomatoes, and garlic to the sheet pan. Cover with the oil, oregano, salt, basil, black pepper, and red pepper flakes and toss to combine, coating the vegetables in the oil and spice evenly.
Bake until the vegetables are soft and browning, 25 to 30 minutes. Let cool on the counter for 10 minutes.
Meanwhile, prepare the pasta. Bring a pot of salted water to a boil, add the penne, and cook until al dente. Reserve ¼ cup of pasta water before draining.
Add the cooled vegetables to a blender or large food processor along with the cottage cheese, nutritional yeast, and 2 tablespoons of the reserved pasta water. Blend on high speed until completely smooth, 45 to 60 seconds. If needed, add additional pasta water to thin.
Combine two cups of the blended sauce with the cooked pasta. Mix and add additional sauce until desired sauciness is reached.
Divide evenly among four plates and top with chopped parsley and grated parmesan, if desired.
