Preheat oven to 400 F°.
Cut peppers in half and remove ribs and seeds. Place cut side up in shallow microwave safe bowl or dish. Add ? cup water to bowl. Sprinkle peppers with kosher salt and cover with plastic wrap. Microwave on high for 5 minutes. Remove and set aside.
Heat large skillet over medium high heat and melt butter and olive oil. Add garlic and cook for 1 minute, stirring after 30 seconds. Add onion and sauté for 2-3 minutes, stirring occasionally. Add butternut squash, thyme leaves and kosher salt and cook for another 5 minutes. Remove from heat. Add 1/4 water. Return to heat and cook for 4-5 more minutes until water has cooked down and squash has softened and is easily pierced with a fork. Keep warm and add Ricotta and Feta cheese. Taste and season with more salt if desired.
Pour marinara sauce in bottom of 9 x 12 inch baking dish. Place peppers cut side up and spoon ½ to ¾ cup of butternut squash mixture into each pepper, creating a hollow for egg. Bake peppers and squash mixture for 10 minutes or until warmed through. Remove from oven.
Carefully break egg into small ramekin or measuring cup and slowly pour into each pepper taking care not to overflow egg. Repeat until each pepper is filled.
Season with freshly ground black pepper and bake peppers for 10-12 minutes or until whites of eggs are set. Serve each pepper with marinara sauce and extra feta cheese if desired.