Preheat the oven to 350ºF. Grease a 2-quart (8 cup) casserole dish.
Make the sauce:
In a medium skillet, sauté the onion and garlic in the olive oil until just browned. Meanwhile, place the spinach, beans, milk, broth, chickpea flour, nutritional yeast, and salt in a food processor. Puree until almost smooth. Add the cooked onion mixture and process again until well combined.
Spread about ½ cup of the spinach sauce over the bottom of the casserole dish, just to cover. Layer half each of the potato, squash, and rutabaga in the pan, overlapping the slices if necessary to create one thin layer of each vegetable. Top with half of the remaining sauce, then repeat the layers and finish with the sauce. Bake for 50 minutes.
While the casserole bakes, make the crumble topping:
In a medium bowl, sift together the flour, baking powder, xanthan gum, and salt. Break the coconut oil into small pieces and scatter it over the flour, then pinch the mixture between your thumb and fingers until crumbly and all the oil is incorporated. Drizzle with the milk, then toss with a fork until it comes together in a moist yet crumbly mixture.
After the casserole has baked for 50 minutes, remove it from the oven and sprinkle with the crumble topping. Bake for another 30-40 minutes, until the vegetables are tender and the sauce is bubbling. Allow to cool 10 minutes before serving.