For The Stuffed Zucchini “Boats”: Place the mushroom caps in a bowl, cover them with the water, and set them aside for at least 30 minutes.
Preheat the oven to 350 degrees F.
Wash the zucchini, trim the stem ends, and split the zucchini in half lengthwise. Using a melon baller or a metal measuring teaspoon, remove and reserve the seeds and flesh, leaving eight oblong “boats” of zucchini with bases and sides about 1/4 inch thick. You should have about 12 ounces (2 1/2 cups) of flesh and seeds; chop this mixture coarsely, and set it aside.
Remove the mushroom caps from the soaking liquid (reserving the liquid), press them lightly to remove excess liquid, and chop them coarsely. (You should have about 1/2 cup chopped mushrooms.)
Heat 2 tablespoons of oil in a large skillet. When it is hot, add the onion and mushrooms. Slowly pour in the reserved mushroom-soaking liquid, leaving behind and discarding any sandy residue from the bottom of the bowl. Bring the mixture to a boil, cover, and boil for 6 to 8 minutes, or until all the liquid has evaporated. Then uncover and cook for another 2 to 3 minutes to brown the onion and mushrooms lightly.
Add the reserved zucchini flesh and garlic, and cook, covered, for 3 to 4 minutes, until soft. Transfer the mixture to a bowl, and let it cool to room temperature.
When the zucchini mixture is cool, add the bread crumbs, 3 tablespoons of the cheese, the parsley, the chives, 1/2 tablespoon of the salt, and the pepper. Toss the mixture gently but thoroughly.
Sprinkle the remaining 1/4 teaspoon of salt on the zucchini “boats”, and stuff them with the mixture, dividing it evenly and packing it firmly but lightly in place. Sprinkle the remaining tablespoon of cheese on top of the “boats”, and arrange them on a baking tray. Bake at 350 degrees F for 30 minutes, then place under a hot broiler to brown the tops lightly.
For The Red Pepper-Tomato Sauce: While the boats are baking, cut the tomato into chunks, and place it in the bowl of a food processor. Seed the red pepper, cut it into chunks, and add it to the food processor bowl with the water, oil, salt, and pepper. Process until the mixture is liquefied, and then transfer it to a small saucepan. (You will have 2 cups.)
Bring the mixture to a boil, reduce the heat to low, and simmer gently for 5 to 8 minutes. Use as is or, for a smoother sauce, emulsify the mixture further with a hand-held blender.
. To serve, place two zucchini “boats” on each plate, and surround them with the tomato-red pepper sauce. Serve immediately.