Fill a large pot with lightly salted water and bring to a rolling boil over high heat. Once the water is boiling, stir in the penne, and return to a boil. Cook the pasta uncovered, stirring occasionally, until the pasta has cooked through, but is still firm to the bite, about 11 minutes. Drain well in a colander set in the sink.
Heat the olive oil in a skillet over medium heat. Stir in the zucchini, bell pepper, carrots, mushrooms, and onion; cook and stir until the onion has softened and turned translucent, about 5 minutes. Add the garlic and cook for one minute more. Stir in the tomatoes, chicken broth, parsley, basil, oregano, and red pepper flakes. Bring to a boil, then reduce heat to low and simmer until sauce thickens. Stir in the pasta and cook until heated through, about 2 minutes. Top with Parmesan and Gouda cheeses before serving.
