Preheat the oven to 425 degrees F.
On a baking sheet lined with parchment paper, toss the peppers, zucchini, butternut squash, mushrooms, and onions with olive oil, 1/2 teaspoon salt, 1/2 teaspoon pepper, and dried herbs. Roast for 15 minutes.
Bring a large pot of salted water to a boil over high heat. Add the pasta and cook for 3 minutes less than box directions. Since you will be cooking the pasta a second time in the oven, you want to make sure the inside is undercooked. Drain in a colander.
In a large bowl, toss in drained pasta and the roasted vegetables, marinara sauce, cheeses, peas, 1/2 teaspoon salt, and 1/2 teaspoon pepper. Using a wooden spoon, gently combine, until all the pasta and vegetables are coated with the sauce.
Pour the pasta into a greased 9 by 13-inch pan. Top with more parmesan and butter pieces. Bake until top is golden and cheese melts, 20-25 minutes.
Note: You can also make this dish Paleo by preparing with Spaghetti Squash. Just bake the spaghetti squash along with the vegetables except for 45-50 minutes.