There is no question that the 72-hours of MTR use starts at your first non-Airport Express use. Not the time you arrive at Central.
However, you did raise a good point about the free transfer associated with the AE trip. That really shouldn't activate the start of the 72-hour either (as long as you do a "valid" transfer with an hour of the AE ride) but I guess you can ask the MTR representative when you purchase the ticket. Or someone else here may have the answer.
[There are also two free shuttle buses at the Hong Kong station to main hotels on the Island.]
[This message has been edited by rkkwan (edited Feb 28, 2004).]