The cars that did not finish a stage were scored as a DNF (look at the championship points give out), the 30 minute time was explained to me as a fix for the scoring system to allow for cars that retired to still get a time in the system for the hillclimb. Cars that DNF'ed the Pro-rally were allowed to take part in the hillclimb portion of the event on Saturday.
For example, Jon Hamilton DNF'ed the Pro-rally on SS1, did not take part in SS2 and SS3 (and SS5 if it had run), but did get to run SS4 which was also for the hillclimb championship.
Dave