Combine zucchini and summer squash in a bowl and sprinkle 2 tablespoons kosher salt over top; toss until everything is evenly coated. Let sit for 15 minutes, tossing occasionally.

Thoroughly rinse squash with cold water to remove all salt; transfer to a colander and let drain for 15 minutes.

Heat 1 tablespoon olive oil in a 10-inch, oven-proof skillet over medium heat. Add bacon and cook until browned and almost crisp, about 5 minutes.

While the bacon is cooking, mix eggs, ¼ teaspoon kosher salt, black pepper, cayenne, and green onions together with a fork in a large bowl.

Raise the heat on the bacon to medium-high; toss in peppers and red onion plus a pinch of salt. Cook and stir until the peppers just start to soften and the onions turn translucent, about 3 minutes. Add drained squash and carefully stir together; cook until squash is just barely tender, about 5 minutes.

Meanwhile, set an oven rack about 6 inches from the heat source and preheat the oven's broiler.

Toss Cheddar cheese into the skillet and pour egg mixture over top. Stir with a spatula (like you were making scrambled eggs) until it starts to thicken up, 30 to 45 seconds. Shake the pan gently to settle the contents and turn off the heat. Push the edges down a bit with the spatula and sprinkle goat cheese over top. Drizzle with remaining 1 tablespoon olive oil.

Place under the preheated broiler until the surface is lightly browned and frittata is firm to the touch, 2 to 3 minutes.

Sprinkle with more green onions and let cool for 5 minutes before transferring it onto a serving plate.