Blend the egg mixture. Add the eggs, cottage cheese, Gruyère, granulated onion, granulated garlic, salt, and pepper to a blender. Blend until completely smooth.
Fill the muffin tin. Line a 12-cup muffin tin with liners and pour the egg mixture evenly into each cup, filling almost to the top. Let sit for a few minutes so air bubbles settle.
Cook the bacon. In a skillet over medium-high heat, cook the bacon until crisp. Drain excess fat, then spoon the bacon evenly over the egg mixture. Top with a little extra cheese and fresh chives.
Prepare the water bath. Place the filled muffin tin on a rimmed baking sheet. Carefully pour hot (almost boiling) water into the baking sheet until it reaches about halfway up the sides of the muffin tin.
Bake. Transfer to the oven and bake for about 30 minutes, until the egg bites are just set in the center. Do not overbake.
Cool slightly. Carefully remove the baking sheet from the oven, then lift out the muffin tin and let the egg bites cool for a few minutes before serving.