Preheat oven to 350F. Put water in a large pot or Dutch oven and bring to a boil over high heat.
Meanwhile grate the soy cheese and set aside. When water is boiling, slowly pour in the polenta while stirring at the same time. Reduce heat to medium-low and continue stirring the polenta every few minutes to avoid lumps and prevent schorching. You may want to partially cover the pot with a lid as the polenta tends to start spitting as it thickens.
It should take about 20 minutes for the polenta to become as thick as porridge. In the meantime, finely chop the green pepper and slice the mushrooms and tomatoes. Heat some non-fat cooking spray in a frying pan, add peppers and mushrooms and saute a few minutes over medium heat until the juices have been released. Drain off excess juice.
When the polenta has thickened, turn off heat and stir in half of the grated soy mozzarella and all of the dried pepper flakes. Transfer the polenta to a 10" by 15" rectangular glass or stainless steel oven pan and spread out evenly. Let cool for 15 minutes while you take a break. When the polenta has sufficiently cooled, spread the pizza sauce evenly over the top, followed by the tomato slices, green peppers and mushrooms. Sprinkle remainder of the soy mozzarella on top of the vegetables, followed by the Italian seasoning. Place dish in oven on lower rack and bake 15-20 minutes until heated through and cheese has melted.