They need to change this rule. The stopping of the clock should have nothing to do with if you have an option or not. So if they gain a first down or not, it should have nothing to do with your option.
Actually, it should.
3-4-3 is designed to prevent a team from gaining a timing advantage by committing a foul. It is not intended to change the natural flow of the game. For those situations in which the clock would have stopped anyway, for some other reason, the team ahead in score gains no advantage that they would not have had by natural flow anyway. This 'option' for the offended team keeps an opponent from committing fouls inside the last 2 minutes of a half that would give that opponent the ability to simply run the clock out, unfairly disturbing the natural flow of the game. This rule removes judgment by the R, inside 2 minutes in each half. Outside of 2 minutes, the R has to make a judgment regarding the intent of the offending team.
With current timing rules, the offending team (ahead in score) would typically hurt themselves by committing a live-ball foul, because the play clock would be 40 seconds, and running - even if a first down. Since the 'goal' for a crew in spotting the ball for the next play is by the 32-second mark of the play clock, the offending team would "shoot themselves in the foot" by some 7 or more seconds if a penalty is completed. So, it would be unusual (perhaps foolish) for a team to intentionally commit a live-ball foul in this situation.
But, without this rule, a winning Team A could get to 4th down with the game clock running, then start committing delays of game, false starts, etc., and keep burning 25 seconds off the game clock until it expired. That is certainly not right for the game. This rule DIRECTS the clock to start on the snap, unless the offended team (behind in score) elects to let the clock run. That might only be in a blowout situation, but they should be allowed that privilege. But to give the offended team that privilege
in all circumstances is not right for the game, either.