IMHO FI 3-4-3-VI does not apply here since it is specifically for a play that ends in bounds with the clock running. Where do we get language that gives B a clock option following a penalty enforcement when the primary reason for the game clock being stopped was not the flag?
Uh, 3-4-3 has that language. The fourth sentence. Unlike the 10-second subtraction associated with the helmet off rule and the injury rule, which specifically state, "...is the only reason for stopping the clock...," 3-4-3 only states, "If the game clock is stopped to complete a penalty for a foul by the team ahead in the score..." Then it goes on to say that the clock will start on the snap, at the OPTION of the offended team.
AR 3-4-3-VI has two parts. One in which the clock is running and is only stopped due to the completion of the penalty. The other - the one to which I refer - has Team A reaching their line-to-gain, which provides an alternate, or, perhaps, 'primary,' as you say, reason for the clock to stop (in addition to the completion of the penalty). The ruling allows the offended team, behind in score, to have the game clock start on the snap at their OPTION.
If the intent is to give the offended team this option only if the game clock would otherwise start on the referee's signal, why doesn't the rule say that? Not exactly rocket science. Heck I can even do that:
"If the game clock is stopped to complete a penalty for a foul by the team ahead in the score (or either team if the score is tied) inside then last two minutes of a half,
and, by rule, the game clock would otherwise next start on the referee's signal, the offended team shall have the option to have the game clock next start on the snap."But, it doesn't say that. Redding & Shaw are smart people. If that was their intent, I believe it would say so. Otherwise, with AR 3-4-3 (b), I believe the offended team can have the clock started either on the snap or the referee's signal, at their option, regardless of the alternate reason for the game clock to stop.
If the score is tied, I can easily see the offended team wanting the game clock to run, especially if they are on defense, and they would like the half to end, to keep Team A from having time to score.