Serial Number Changed After Genius Bar Repair

They should have told you that, but often they just do complete replacements in lieu of repairing an actual device. I'm sure that's pretty much the only way they would handle case damage. Then they'll evaluate the exchanged device for whatever parts can be reused to make refurbished devices.

Did you back up and then wipe before you brought it in? I should be pretty obvious if it's a replacement device, because the model number should start with an N. A device that was sold as a new retail device will have a model number that starts with N. That's in Settings > General > Model Number. It's usually right there, but if you see a model number that starts with an A, you can tap on the model number to switch between the AXXXX number of the full model number. The replacement device can be new or refurbished from used, good parts, but often come with new cases/displays and always come with a new battery.

However, in my experience they'll usually bring out the "white box" replacement device and perhaps ask if the user would like to transfer the data from the exchanged device. It seems unusual that this was done in the back.

The numbers are not the same because you were given a replacement phone. That's standard practice when the damage is too severe to reasonably 'repair' the original device.