I'm quite curious to know what the rules would be for individual maps, mainly because there is a grey area in where to stop the clock in certain cases.

Personally I think the timer should start as soon as the mission briefing appears and end when the last crystal is counted on a map.

This doesn't clear up maps like The Path To Power, however. Completing the Power Station has a delay of a few seconds (due to the message being played) before the game counts the mission as finished.

Another case in point would be locating trapped Raiders or guiding them home (Breathless, Search 'n Rescue, Run the Gauntlet).