These folders are not made/used by the system during user creation because the system doesn't generate them. They are generated the package
xdg-user-dirs-update (Ubuntu) and
/usr/bin/xdg-user-dirs-update is run at logon and creates the files based on defaults in
/etc/xdg/user-dirs.defaults, or if it exists
If you want to disable it, the setting is in
/etc/xdg/user-dirs.conf, or uninstall the package, if dependencies allow.
Reference: Who is creating Documents/Video/Pictures/etc. in home directory