Preheat oven to 350°F. Spray a 9x9-inch baking dish with nonstick cooking spray. Set aside.
Line a baking sheet with paper towels. Lay sliced tomatoes on the lined baking sheet. Sprinkle with 1 teaspoon kosher salt. Let sit for 20–30 minutes to draw out moisture. (This helps prevent a watery dish.)
In a medium bowl, combine mozzarella, cheddar, parmesan, mayonnaise, oregano, garlic powder, remaining ½ teaspoon salt, black pepper, and cayenne. Mix until well blended.
Spread about 1 cup of the cheese mixture into the bottom of the prepared baking dish.
Arrange the tomato slices in a single, slightly overlapping layer over the cheese mixture.
Sprinkle chopped basil and green onion evenly over the tomatoes.
Spread the remaining cheese mixture evenly over the tomato layer, covering as much of the surface as possible.
Sprinkle the crushed crackers evenly over the top.
Bake, uncovered, for 35–40 minutes, or until the top is golden and bubbly.
Let cool for 5–10 minutes before serving.