Preheat the oven to 350 degrees Fahrenheit and grease a large baking dish with cooking spray.
In a large bowl, whisk together the eggs and milk until light and frothy. Set aside.
In a large skillet over medium heat, cook the turkey bacon until crispy. Transfer the slices to paper towels to drain. Pour off most of the bacon fat, leaving about 1 tablespoon in the skillet.
Pour the egg mixture into the skillet and immediately lower the heat to medium-low. Stir occasionally with a spatula or wooden spoon. When the eggs are almost set, season with salt and pepper, then fold in the chopped chives. Remove from heat.
Spread cream cheese onto the bottom halves of the bagels, then arrange them side by side in the greased baking dish.
Spoon the egg mixture evenly over the bagel halves, then crumble the cooked turkey bacon on top.
Sprinkle with shredded Cheddar cheese, then place the bagel tops over the cheese.
Brush the tops with melted butter and sprinkle with dried onion, granulated garlic, sesame seeds, and poppy seeds.
Bake until the bagels are toasted and the cheese has melted, about 10 minutes.
Serve warm.