Preheat the oven to 375 degrees.
Place the eggplant slices on a paper towel-lined rimmed baking sheet. Sprinkle both sides with salt. Let stand while preparing the tomato sauce.
Heat 1/4 cup olive oil in a deep 12-inch oven-safe skillet or braiser over medium heat. Add the onion, reduce the heat to medium-low, and cook for 6-7 minutes, or until softened.
Add the garlic and oregano and cook for 30 seconds, stirring constantly, until fragrant.
Add the crushed tomatoes. Swirl the water in the empty tomato can, then add it to the skillet. Bring to a simmer and cook uncovered for 8-10 minutes, or until slightly thickened.
Stir in the beans, basil, and crushed red pepper flakes. Season to taste with salt and freshly ground black pepper.
Arrange the red bell pepper in an even layer over the tomato-bean mixture.
Pat the eggplant thoroughly dry, removing excess moisture and salt. Arrange the slices over the peppers in an overlapping circular pattern.
Lightly season the zucchini and yellow squash with salt and black pepper. Arrange them in overlapping circles over the eggplant, alternating the slices if desired.
Cover and bake for 1 hour, or until the vegetables can be pierced with a knife.
Combine the panko, Parmesan, and remaining 1 tablespoon of olive oil, stirring until the crumbs are evenly moistened. Sprinkle evenly over the vegetables.
Return to the oven and bake uncovered for 20 minutes, or until the topping is golden brown and the vegetables are bubbling around the edges.
Let stand for 10 minutes before serving.