Preheat oven to 400 degrees.
Heat 1 tablespoon of oil in a large skillet over medium heat and cook onion until it begins to soften, about 3-5 minutes. Add all of the chard (or in batches if it's too big for your skillet) with a large pinch of salt and cook until chard is wilted and all moisture is evaporated. Transfer to a bowl and set aside.
In the same skillet over medium heat, add remaining oil and flour and whisk to combine. Pour in the soy milk, whisking constantly until thoroughly blended. Add garlic and nutritional yeast and let come to a boil, whisking, for 2 minutes so that sauce can begin to thicken. Remove from heat, season with 1/4 teaspoon salt and plenty of cracked pepper.
Lightly oil a casserole dish and lay half of the sweet potatoes, slightly overlapping, in a layer. Sprinkle half the beans over the potatoes, topping with some nutmeg, salt, and pepper.
Next, spread half the greens over the beans and pour over half the sauce. Repeat, layering potatoes, beans, seasoning, greens and sauce. Top with the almond parmesan.
Cover with tin foil and bake for 45 minutes, remove foil and bake for 15 more. Casserole should look nice and bubble. Let sit for a few minutes before serving.