If using bacon, cook bacon and drain and chop. Set aside. Butter a 9x13" baking dish and set aside.
Combine the butter and oil in a large sauté pan over medium heat. When hot, add the onions and toss to coat in the butter. Season with kosher salt and freshly ground black pepper. Cook the onion, stirring occasionally, until the onions are golden brown and caramelized. When the onions are nearly done cooking, add the mushrooms and cook until the mushrooms are tender and the onions are done. Remove from heat.
Preheat oven to 325 degrees F. Spread bread onto the baking sheet and bake for 10 minutes, stirring once halfway through. When lightly toasted, spread the bread into the prepared baking dish. Sprinkle with bacon, then add the mushrooms and onion mixture the drained spinach, and 1 1/2 cups of the shredded cheese and toss to evenly distribute the ingredients.
In a large bowl, whisk together the eggs, milk, cream, mustard, 1/2 teaspoon kosher salt, 1/4 teaspoon freshly ground black pepper, and nutmeg. Pour the mixture evenly over the bread mixture. Cover the baking dish and refrigerate for 2-24 hours.
When ready to bake, preheat oven to 350. Uncover the baking dish and bake until the mixture has puffed up and the top is golden and the strata doesn't jiggle when you shake it (about 1 hour). During the last 10 minutes of baking, add the reserved 1/2 cup of cheese. When done, remove from the oven and allow to stand for 10 minutes before serving. Use a spatula or serving spoon to dish out the casserole and then top with the sautéed cherry tomatoes.
To prepare the cherry tomatoes, heat the oil in a large sauté pan over medium heat. When hot, add the tomatoes, season with salt and pepper, and cook until the tomatoes begin to soften (about 5-7 minutes). Remove from heat and stir in the chives. Serve on top of the strata (or alongside your favorite breakfast foods).