I suppose another bit someone should check, is how different (if at all) the Uno bootloader is because of the change in the USB comms chip.
We moved to github to make it easier for the community to contribute to the project.
I just compared the code. Nothing in the '328 bootloader changed.
Please note that the Arduino VID and PIDs are only for use with official Arduino hardware and should not be used on other products.
It looks like Uno uses the new optiboot, which is also open source, and it one of the several new bootloaders in the 0020 download.
I suppose the only significant issue would be if newer Arduino bootloaders are made reliant on the 8u2, thereby making non-8u2 based boards require different bootloaders.
Having read this code, I would say any such fears are utterly unfounded. Did you read the code? I have, and there doesn't seem to be anything like this.