I don't see how standbys can be dealt with anywhere other than the gate.
I used to be a check in agent. On the occasion we had standby passengers due to oversales, even after accepting people once check in closed (by removing seat assignments for people who didn't check in), we would still send the odd few to the gate even if the flight was then full. You get a lot of people who don't turn up airside, even after checking in at the airport. Quite often you would get down to -10 minutes before STD and if passengers didn't show up after numerous calls, they get offloaded and the person on standby would get on instead. If we didn't allow at least a few standbys to go right to the gate then most oversold flights would still leave with empty seats. Offering the customers incentives several hours before the flight wouldn't really work, airlines would be paying out more DNB than necessary as it would more often than not backfire. That would merely cause them to oversell flights more.
The system they use now is not 100% accurate, but it's as best as you'll get unless you can absolutely guarantee every single person who is checked in gets on the plane on time.