I'll reiterate - checkpoint progress is irrelevant. There are only two states of the crystal that matter: 50% progress - the crystal is on the checkpoint - and 51% progress - the checkpoint has been broken and the crystal moved past it.

If the winning team reached 50% but didn't manage to break checkpoint before overtime started the only way for the losing team to win is to completely break the other checkpoint and get to that 51%. And it is a loss the moment you all step off the crystal for 3 seconds before you do it. Regardless of how much progress you might have made to breaking the checkpoint.