The deduplication is only for one specific version, even if its installed on my operating system already. AppImages do not include the entire KDE system. And Flatpak will install multiple versions of drivers (Mesa in example) and other dependencies. While this is exactly what Flatpak was designed for and there are good reasons for, it is important to understand that was counter arguing your argument against AppImages for being bloated. Both approaches are good in their own way, depending on what you want or need.

The backup of Yuzu Flatpak was just a current example why someone would want do that. There can be any reason to backup specific software versions, which is not the topic of today. The topic is, that with Flatpak its a mess to backup and restore. Yes, you can copy the configuration and installed binary files, but that does not work on any other computer. You can backup the key and other important files as well, but then its complicated to restore them as well, that I just gave up. It's probably not impossible, but not straight forward; a bad user experience.

Meanwhile I can just download an AppImage and copy the file and its archived. Done. In multiple versions. No extra software, knowledge or complicated dance to do this very simple and important task.