Since hang time on punts and kickoffs are both around 4 seconds, I think the rule should be consistent. If a team calls a timeout before punting, the clock starts when the ball is snapped. Along the same lines, the clock should start when the ball is kicked. Who is to say that clock operators can really tell when an onside kick is legally touched? Conversely, it is very easy to see when a ball is kicked and when the play is dead.
Had the old timing rules been in affect during yesterday's Bills game, the results may have been different and the coaches wouldn't be questioned.