Combine zucchini and summer squash in a bowl and sprinkle 2 tablespoons of kosher salt over top; toss until 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, 1/4 teaspoon kosher salt, black pepper, cayenne, and green onions together with a fork in a large bowl.

Raise heat on the bacon to medium-high; toss in peppers and red onion plus a pinch of salt. Cook and stir until peppers just start to soften and 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 until it starts to thicken, 30 to 45 seconds. Shake the pan gently to settle contents and turn off the heat. Push edges down with a spatula and sprinkle goat cheese over top. Drizzle with remaining olive oil.

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