Cook the pasta according to the directions on the package, adding a generous tablespoon or so of kosher salt to the water as it cooks. Drain, but do not rinse.
While the pasta is cooking, warm the oil in a large deep-sided skillet over medium-high heat. (I like this skillet!) If a deep skillet isn't available, a dutch oven or large pot will also work. Add the onion to the skillet and cook for a minute before adding the peppers. Continue cooking, while stirring frequently for 2 minutes. Add the broccoli and cook 1 more minute before adding the mushrooms and both squash.
Continue cooking and constantly tossing the vegetables for 3-4 minutes until barely softened and still crisp-tender. The skillet will be very full and stirring constantly avoids overcooking the vegetables on the bottom of the pan.
Remove the vegetables from the heat and season to taste with salt and pepper. Transfer the vegetable mixture to a bowl or plate.
Combine the olive oil, pepper flakes, salt, and garlic in the empty skillet or pot. Stir while heating the pan over medium-high heat. Saute for about 30 seconds, just until everything is fragrant. Stir in the tomatoes and heat to a gentle simmer, this should only take a couple of minutes.
Taste the sauce. If it needs more salt, add it now. Stir in the lemon zest (if desired and if not using meat) and taste again. Add the pasta to the sauce and toss well.
Return the vegetable mixture to the skillet and toss to combine. (Add the cooked meat, if desired.) Sprinkle with parsley. Serve warm.