You can customize those 'well known' directories.
https://www.freedesktop.org/wiki/Software/xdg-user-dirs/
The Arch wiki has more instructional docs:
https://www.freedesktop.org/wiki/Software/xdg-user-dirs/
The Arch wiki has more instructional docs:
Other "new" softwares that fail to follow best-practices by putting top level files into ~/ just on my laptop are: npm, Ansible, pylint, docker, steam, rustup+cargo, vscode, IDEA IDE, Zoom, AWS CLI. These applications have no excuse.
Also I agree on the Documents, Music, Video, etc. I hate upper case letters in my folders, so when I do a reinstall I delete those and restore my backups from the lower-case versions.