Isn't that pretty much just Windows? That basically never occurs on Linux and it's not common on macOS, either. All the garbage I have on my work computer (a Mac) in ~/Documents is stuff that OneDrive synced over from when I used to have a Windows computer there. (If I could turn the OneDrive feature that takes over ~/Documents and ~/Downloads, I would.)

Linux software is notorious for spewing crap all over the user's home directory. Delete everything inside your /home/name and see how well the system still works. On iOS/iPadOS nothing happens other than not having the documents you saved in there.

I'm not sure there even is a good place where programs can store their internal system files without requiring root other than mixed in with the user Home.