The rule makes sense.
Typically after an incomplete pass, a second or two runs off the clock before it stops. It's sort of been a gray area at the end of games where refs will sometimes review the tape and stop the clock on the *EXACT* second the ball hits the ground. Sometimes, the refs do this, and sometimes they treat it like they do the entire game (allowing a second or two to run off).
My guess is that they enacted the rule to eliminate the 'referee discretion' aspect of it. If you hike the ball with under 3 seconds, it should theoretically take off at least a second to run the play, and maybe another 1-2 seconds of clock run-off. Instead of leaving it to the individual refs to decide how to treat the situation (with many refs taking different positions), they set one uniform rule across the board.