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 frypan over medium heat. Stir in the zucchini, capsicum, 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 stock, parsley, basil, oregano and chilli 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.