System crontab is a great way for distro maintainers and app packagers
to include cron jobs that don't pollute the user crontab space.
The system crontab files can specify a user to run as, so not everything
in the system crontab has to run as root.
Non-login-users don't have crontabs, so the only place to put
non-login-user tasks is in the system crontab.
Generally, you would put local/custom stuff in the root (or appropriate
user) crontab, while prepackaged stuff that you don't directly maintain
lives in the system crontab.
Really, it's just a matter of organization