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Place racks in the upper and lower thirds of your oven and preheat to 425 degrees F. Lightly coat a wide 3-quart casserole dish, such as an 9x13, with nonstick spray. Line a rimmed baking sheet with foil.
In a large bowl, toss the cauliflower florets with the olive oil, garlic powder, salt, pepper, and nutmeg. Transfer the cauliflower to the prepared casserole dish and spread into an even layer. Keep the bowl handy. Bake the cauliflower on the lower rack for 30 minutes, until the florets are tender and begin to brown.
Meanwhile, arrange the bacon strips in a single layer on the prepared foil-lined baking sheet. Bake on the upper rack until crisp, about 10 to 15 minutes. Remove the bacon and cauliflower from the oven. Stir the cauliflower, spread it back into an even layer, and place it on the upper rack to continue cooking until the end of its baking time. Transfer the bacon to a paper-towel-lined plate and lightly pat dry. Once cool enough to handle, roughly chop or crumble the bacon into small pieces.
In the same bowl that you used to toss the cauliflower, beat together the cream cheese and Greek yogurt until combined. Stir in 1/3 cup gruyere cheese, 2 tablespoons Parmesan cheese, and half of the chopped bacon.
Remove the roasted cauliflower from the oven and dollop the cream cheese mixture over the top. Sprinkle with the remaining 1/3 cup gruyere and 2 tablespoons Parmesan. Return the pan to the upper third of the oven and bake until the cheese is melted and gooey, about 5 to 7 minutes. Turn the oven to broil. Broil the casserole until golden on top, 1 to 3 minutes. Do not walk away, and watch carefully to make sure the cheese does not burn. Remove from the oven and sprinkle with fresh chives and remaining bacon. Serve hot.