I think the idea of checking-in is to deal with the possiblility of last-minute flyers.

Lets say an airplane has 100 seats on it. They've assigned 70 of those seats before the day of the flight. But they sold 103 tickets, thinking that there would be three no-shows. However, four people do not show up for their flight. 30 minutes before flight time, 99 people have checked in. That means they can say that at a specific moment in time, they have a single seat available for a last-minute customer and that anyone who has "checked-in" after the cutoff point, even if they have a confirmed reservation, is no longer guaranteed a seat. This make sense?