Yep, if the clock was stopped ONLY to complete a penalty by the team ahead in score, then the opponent would have the option to start the clock on the snap. But, in the case presented, when the RO ruled the BC was down in the field of play, officially, the clock was stopped for the first down, as well as to complete the penalty for A's foul; so B doesn't have an option. Start the game clock on the R's signal. No option for a ten-second subtraction, either.
The R has the discretion to start the clock on the snap for an obviously unfair act. But Team A is not fouling to manipulate the clock, in this case, so the clock should follow standard rules.
Robert