Spray a 9-by-13-inch baking dish with nonstick cooking spray. Spread the bagel chunks in the dish in an even layer, then dollop the cream cheese around the baking dish, on top of and in between the bagel chunks.
In a large bowl, whisk together the milk, eggs, garlic powder, salt, pepper, half the red onion and half the chives until combined. Pour the mixture over the bagels in the baking dish. Cover the baking dish with foil and refrigerate overnight.
Preheat the oven to 350 degrees F. Set the baking dish out at room temperature while the oven heats.
Bake, still covered in foil, until mostly set, about 1 hour. Remove the foil and bake until the top is lightly browned, 10 to 15 minutes more. Let cool slightly for 10 to 15 minutes. Garnish the top with ribbons of smoked salmon, capers and the remaining red onion and chives. Serve immediately.