Remove the thyme stems from the skillet and drain off any water or oil still in the pan.
In a small bowl, combine almond flour and softened butter with a fork or your hands until it turns into a paste.
In a large bowl, combine cooked squash and onion mixture, cheddar cheese, mozzarella cheese, parmesan cheese, heavy whipping cream, egg, garlic powder, onion powder, and cayenne pepper. Stir well to combine.
Pour into a baking dish.
Top with dollops of the almond paste and a sprinkle of paprika.
Bake for approximately 40 minutes, until the top is golden brown and bubbly.