Preheat oven to 400 degrees F (200 degrees C). Lightly grease an 11x13-inch glass baking dish baking with olive oil.
Melt 5 tablespoons butter in a saucepan over medium-low heat; cook until bubbling and beginning to brown, 2 to 3 minutes. Stir arrowroot flour into the butter until completely moistened; season with 1 teaspoon marjoram, salt, black pepper, and nutmeg.
Pour almond milk over the arrowroot mixture, whisking continually to integrate. Bring mixture to a boil, stir ricotta cheese into the mixture until smooth, and immediately remove saucepan from heat.
Pour about 1/3 of the ricotta mixture into the prepared baking dish and spread into an even layer. Layer about half the butternut squash, kale, and onion atop the sauce, respectively; top with about 1/2 of the ricotta mixture. Layer remaining squash, kale, and onion over the second layer of ricotta mixture and then cover with remaining ricotta mixture. Cover the dish tightly with aluminum foil.
Bake in preheated oven until the squash is tender, about 30 minutes. Remove and discard aluminum foil.
Mash the almond meal, nutritional yeast, 5 tablespoons butter, Parmesan cheese, 1/2 teaspoon marjoram, thyme, and sea salt together with a fork or pastry cutter; spread in a layer atop the gratin.
Continue baking until the gratin is bubbling and the topping is browned, 5 to 10 minutes.