Scenario 1
If your team reaches the checkpoint before the clock runs out while your opponent's team has not reached the checkpoint before the clock runs out, the opposing team can not leave the crystal and must stay on the crystal until they reach the checkpoint, clear the checkpoint, and move the crystal to 50.1% or they lose.

Scenario 2
If both teams have reached the checkpoint before the clock runs out but neither team has cleared the checkpoint, once overtime starts both teams are able to leave the crystal without losing the game. However only the team that both breaks the checkpoint AND moves the crystal to 50.1% will be declared the victor.

Note about scenario 1: it is very important to keep track of whether each team has reached the checkpoint before or during overtime. Often times a losing team will push the crystal to the checkpoint DURING overtime, then fall back to regroup and immediately lose the game.

Note about scenario 2: There are times where your team is the first to clear the checkpoint but your party wipes. Just because you cleared the checkpoint does not mean you will be the victor. You must also push the crystal that extra 0.1% otherwise the opposing team now has an opportunity to also clear the checkpoint and push 0.1% to win the game.

Hope this helps, was just chilling here eating breakfast and thought I'd chime in lol.