I know not everybody has an external case, but many of those who replace own HDs do. They can (as I do):
Use Carbon Copy Cloner to backup / prepare for system upgrade.
Sure, that’s when you have a working and bootable backup. If you don’t (for example because you are using Time Machine) it’s not really clear what you do.
I think Apple has thought of some solution, we just don’t know it yet. It’s an interesting question.