Bring a medium pot of salted water to a boil. Add the squash and cook 5 minutes or until just becoming tender. Drain well in a colander and let cool for a few minutes.
While the squash is cooling, melt 2 tablespoons of butter in a small saucepan over medium high heat. Add diced onions and cook until translucent. Remove from heat and let cool slightly.
In a medium sized bowl, combine almond flour, remaining butter (melted), 2 oz cheese and salt for crumble topping.
In a large mixing bowl, combine squash, onions (and the butter they cooked in!), 6 oz cheese, and eggs. Pour into a greased 9 x 13 inch casserole dish.
Add crumble topping to the top of the casserole, crumbling with your fingers.
Cook 30 minutes or until egg is set and edges and topping are beginning to brown.