Preheat oven to 375 degrees. Grease a glass 8x8 pyrex dish.
Heat a heavy bottomed pot over medium high heat and add butter. Stir in sliced onion and cook until translucent and softened, stirring often, for 5 minutes. Stir in sliced squash and a generous sprinkling of salt, pepper and granulated garlic. Add filtered water and reduce heat- cover pot. Cook for 10-15 min until squash is very soft. Drain well but don't rinse and return squash to pot. Set aside off the heat.
While squash is cooking, make the casserole custard. In a large bowl, whisk together bone broth, eggs, coconut milk, nutritional yeast, melted butter and remaining seasonings. Set aside.
Next, make the crumble topping. In a small bowl, combine all ingredients until a lightly moistened crumble-like topping is formed. Set aside.
After squash is cooked and drained well, spoon a large scoop of warm squash into the custard, stirring quickly. You want to slowly add squash spoonfuls to temper the custard so the eggs do not scramble. Slowly continue to stir in squash until well combined. The mixture will seem thin but it will all firm up completely in the oven.
Transfer filling to casserole dish, smoothing uniformly all over. Next, cover casserole uniformly with crumble topping.
Bake on the middle oven rack for 40-45 minutes, until golden brown and bubbling, rotating pan 180 degrees 2-3 times throughout cooking. Let casserole cool 10 min before serving.