I've never used the airport express check-in, but I will say that it is especially easy to take luggage on the airport express to HKG. The trains usually have empty seats and there are luggage racks. There are escalators and elevators, so no need to lug luggage up/down stairs.

For those of you like me who prefer to sit facing forward, be aware that the train changes direction at the Hong Kong station.

It's actually much cheaper to take the regular MTR line to Tung Chung (?) then take a taxi from there to the airport (e.g., for two people, the airport express might be 200 HKG, but the other route is only about 80 HKG). Of course, these trains are not as comfortable, there's no luggage rack, and it's a bit slower.