The warning is there to tell player that he'll lose the game if he doesn't make moves in xx seconds. It doesn't matter which timing you are using. It does not neccessary to be a sound. The important thing is player notices that he may has time issue.
What does it do with how you organize your time in main?
Van Zeist is not losting on time because he did have enough time to make his move, it's because he's unware of lacking of time.