Preheat the oven to 400° F.
Heat 1 tablespoon of the olive oil in a medium skillet over medium heat. Add the onion and garlic and cook, stirring, until the onion is tender and lightly browned, about 8 minutes.
Stir the water and tomato paste together in a small saucepan and add the herbs. Bring to a boil. Cover the pan and lower the heat to low, simmer for 10 minutes.
While the onion and broth are going, wash the vegetables and cut them on a slight diagonal into ½-inch or so rounds.
Using your fingertips, rub the panko, Gruyere, Parmesan and the remaining tablespoon of oil together in a small bowl until the oil is absorbed.
Grease an 8 x 8-inch square baking dish with olive oil. Spread the softened onion and garlic in the bottom of the dish. Make a row of eggplant slices, slightly overlapping them.
Repeat with zucchini, yellow squash, and tomatoes. Keep making alternating rows of vegetables until the dish is full. The vegetables should be fairly snug but not crammed into the dish. Strain the herb broth over the vegetables. Season the vegetables with salt and pepper. Cover the dish with aluminum foil and bake until the vegetables are tender, about 40 minutes.
Remove the foil, crumble the topping over the vegetables and bake, uncovered, until the topping is golden brown and the vegetables are very tender, about 20 minutes. Let sit at least 10 minutes before cutting and serving (good at room temperature, too). To make nice, neat slices of the gratin, make sure to cut the layers of vegetables all the way down to the bottom and sides of the dish before trying to lift them out.
