Imagine a system where you are just an end user, one of hundreds or even thousands, and the admin removes an application. I would be furious if the admin would also delete my personal application data from my homedir. There could be important settings in there, that I might want to move to another system, or maybe I’ll install my own flatpak in my homedir and continue to use those settings. There could be stuff in there that’s important and for which no backup exists.
So how would you implement that: would you, while uninstalling a system flatpak, be given the option to only remove your personal files and leave the files in other homedirs intact? Or should it remove the files for all other users too, without their permission? In my opinion the best way is to just leave the files alone. I think it makes sense and I think using a 3rd party app to remove the remnants is fine. It works the same on Windows, MacOS and Linux. Maybe adding something to the OS to detect these files and ask each user independently would be a nice addition, but not as part of the uninstall process of the flatpak.