You can still check in at HKG Island or Kowloon, pay the Express fare and still use the executive car. You don't have to phyiscally travel with them but they do deduct the Express fare as you get to the check-in area.

Which personally strikes me as unnecessary, the Express gets nearer to security than the car does, on the same level, and is a lot faster/smoother/less congested/better airconditioned/more spacious/safer blah blah. It's a very slick service as one would expect in HKG. So personally I would take a rickety taxi to the Airport Express at a time of your choosing and then spend as long as you like airside.