Desktop OSs are the worst for mixing random system files with the users own documents. Theres a better balance now where the “Files” app has your documents, downloaded stuff and similar, while system and app data is hidden.

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.)