Like others said, it is a promotion. "Use the Airport express and we will handle your bags for you" - it is quite a valuable perk, as the alternative would be to store bags somewhere in HK. That cost could be more than the ticket itself, if you have a few bags and need storage for a day.
Using the in-town check-in without riding the Aiport Express is using a service but denying the provider any revenue. Not fair. And as I said in first post, the savings by going with some other provider to the airport is small.
I'd hate it if they felt the need to made the in-town check in more restricive or start with random ticket checks or something else.