Yes, the Rules Committee made any foul inside 2 minutes in a half ‘automatically’ qualify for rule-specified clock control, at the option of the offended team, taking that judgment out of our hands - thankfully.
But, outside 2 minutes, a holding foul is not exactly an obviously unfair tactic to conserve or consume time, which is what 3-4-3 is intended to address. Unlike a false start, offside with contact, an illegal forward pass, etc., a player/team can’t necessarily bank on a holding/block in the back/PI, etc., foul getting called, and causing the clock to stop. Those are just normal game play fouls, and shouldn’t be cause for changing game timing. The offending team didn’t do anything ‘obviously unfair’ to alter game timing.
***ADDED 1:45 pm: Of course, there are always extreme cases, such as the Cal defensive holding situation a couple of years ago, which was done purposefully to 1) keep the opponent from scoring, and 2) make the game clock eventually expire, even if only 4 or 5 seconds at a time. As we know, per AR 9-2-3-II and III, the game clock is to be re-set to the original time the down began in these cases, eliminating the advantage that the fouling team would gain. But, again, a holding foul by a teammate of a Team A BC attempting to score is more likely to be trying to help the BC advance and score (and hoping he gets away with the illegal hold) than consciously attempting to get the clock to stop, i.e., not an obviously unfair act to consume or conserve time.***
The guidance is to ‘consider’ invoking this rule inside 5 minutes, not automatically invoke it. Yeah, a non-judgment foul like a false start, etc., should get serious - nearly automatic - consideration. But not a high-judgment foul like holding.