Meanwhile, drain the tomatoes (reserving the juice for another use if desired). Heat 1 tablespoon of the olive oil in a medium saucepan over medium heat. Add the garlic and crushed red pepper flakes and cook, stirring, until aromatic, 1 to 2 minutes. Crush the tomatoes with your hand, adding them to the saucepan as you go. Season with salt and pepper. Add the basil and parsley sprigs (reserve the chopped herbs for later) and bring to a simmer over medium-high heat. Reduce the heat to low and cook at a very low simmer for about 15 minutes or until ready to serve.
While the sauce cooks, heat a large double-burner grill pan over medium-high heat. Toss the pepper, squash, zucchini and onion with the remaining tablespoon olive oil, making sure to coat all sides. Sprinkle with salt and grill, turning once, until well-marked and crisp-tender, 4 to 6 minutes per side, depending on the vegetable. Transfer the onion to a large mixing bowl. Transfer the pepper, squash and zucchini to a cutting board and cut crosswise into strips. Add to the bowl with the onion and cover with foil.
Cook the penne in the boiling water according to package directions. Drain and add to the bowl with the vegetables. Remove the herb sprigs from the sauce and stir in half of the chopped herbs. Add to the bowl and toss to coat.
Serve the pasta in bowls topped with the remaining chopped herbs and Parmesan.