That's the primary difference between the two scripts:
rss-top-warning.php displays nothing if there are not active Watches, Warnings or Advisories. If there is one, it displays the one most severe advisory found (Warning, Watch, Advisory, Special Weather Statement in that order)
rss-advisory.php displays 'There are no active watches, warnings or advisories for zone ssZnnn' if there are none. If there are alerts, it will display the entire list of alerts for the area.
It's your choice whether to use one or the other script. For 'display nothing if nothing to say', select the rss-top-warning.
Best regards,
Ken