This rule might be around to address a situation like:
Team A calls timeout at 7:30 in the 2nd quarter. (Time is marked down by officials).
Team A runs the ball up the center, quick play, Team A huddles and coming out of the huddle they look at the play clock, it's at :07 (with 7:12 on the game clock). The team hurries to the line, to hike it in time before the play clock expires and the line can't block, the QB is almost sacked, but gets the ball away towards a receiver and the ball is thrown incomplete.
7:00 left on the clock.
The coach then looks puzzled at why the team ran out of time on the play clock, why the play was a mess, etc. - then realizes that they should still have until 6:50 to hike the ball.
This should be something that could easily be remedied by the referees as they have the time for the timeout marked on their cards and one official can say that, yes, the play clock was at :01 when the ball was snapped. The math doesn't make sense, so the referee can have authority over this and correct it.