Make the stuffing: Cut shrimp and scallops in three pieces. In a food processor, blend shrimp, scallops, 2 sliced calamari tubes and garlic into a coarse paste. Transfer to a bowl. Then add cheese, parsley, red pepper flakes and season with salt and pepper. Mix to combine.
Make stuffed calamari: Using a small spoon, start stuffing the calamari tubes until almost full and shapely, leaving just 1/2 inch opening, pierce and secure with the toothpick.
To blanched tomatoes: Using a sharp knife, cut an “X” on the bottom of each tomato, it will help to loosen the skin. Place them in rapidly boiling water for 1 minute, then plunge the tomatoes into an ice bath with the slotted spoon. Let them cool slightly, peel the skin off. Chop the tomatoes finely.
Make the sauce: Heat the oil in a large wide-sided skillet, add onions and sauté for 5 minutes until translucent. Add garlic and cook for 1 more minute. Then add tomatoes and sugar, season with salt and pepper and cook for 10 minutes on medium heat.
In a single layer, place stuffed calamari on top of the sauce, cover with the lid and cook for 20 minutes on medium-low heat.
Make polenta: Meanwhile, bring the water to a boil, add polenta, bring back to a boil. Reduce the heat to low and cook for 8 minutes, stirring constantly. Season with salt and pepper.
Serve calamari either sliced on the bias or intact on a bed of polenta with the tomato sauce. Sprinkle with finely chopped parsley and extra serving of Parmigiano-Reggiano cheese on top.