Preheat the oven to 375 degrees F. Grease a 9x13 baking dish or casserole dish with olive oil.
Blanch the green beans: Bring a very large pot of water to a boil and liberally season with kosher salt (about 1 TBS per quart of water). Prepare an ice water bath and set out a large, clean kitchen towel. Place the beans in the water and cook just until tender, about 4-5 minutes. Plunge into an ice bath to stop the cooking, then drain and transfer to the towel. Lightly pat dry.
Make the crispy onion topping: Heat a large saute pan over medium-high heat until hot. Add the olive oil, thinly sliced onions and a pinch of salt, and cook, stirring occasionally, for 7-8 minutes, or until they are tender and slightly brown. Remove the onions and transfer to a mixing bowl. Reduce the heat to medium-low. In the same pan you used to cook the onions, add the almond meal. Cook, stirring very frequently, for 2-3 minutes, or until the almond meal starts to turn lightly golden. Careful not to burn. Remove from heat and transfer the toasted almond meal to the bowl with the onions. Stir in parmesan cheese, parsley and salt, then toss the mixture until combined. Set aside.
Make the creamy mushroom sauce: In the saute same pan, heat the remaining 2 tablespoons of olive oil over medium heat. Add the mushrooms and cook for 5-6 minutes, or until they are tender, stirring occasionally. Add the garlic, thyme and a pinch of salt, and cook for an additional minute until fragrant, stirring frequently. Sprinkle the flour over the mushrooms, and stir to combine. Cook for 1 minute to get rid of the raw flour flavor. Slowly add the milk, whisking to combine until smooth. Season with salt, pepper and nutmeg. Bring the mixture to a simmer. Let cook for 2-3 minutes, or until thickened. Remove from heat and stir in the yogurt until combined.
Assemble: Transfer the cooked, chilled green beans into the pan with the mushroom sauce and toss until combined.Pour the green bean mixture into the prepared baking dish and then top with the crispy onion topping.
Bake: Bake uncovered, for 25-30 minutes, until the top is golden brown. Sprinkle with fresh parsley and flaky sea salt, if desired. Enjoy!