I'm sure that they have a good system. My point is tolerance stacking. On a rifle with a barrel mounted front sight and a receiver mounted rear sight, mechanical zero does not necessarily equate to true zero. (In fact, it almost never does, in my experience.) Assuming that the sights are mounted perfectly (they're not), and that the barrel is timed perfectly (it's not), there's still going to be a small but necessary amount of slop between the barrel and the receiver. Any of these areas will have tolerances involved with them to make sure that Part A from Rifle A will fit Rifle B with no modifications. Murphy's Law dictates that tolerances will stack in the worst possible way more often than not.
Now, assuming that our armorer is on the ball and sights in the rifle perfectly (he won't, on account of being human, but he may very well do an excellent job of it), do I use the same hold and sight picture that he does? Do I shoulder the rifle at the same point, with the same amount of firmness? Do apply the same amount of pressure to the fore end? Am I going to be using ammunition from the same lot that he did when sighting it in? Of course not. All of this will make a difference on the target - less of a difference than a poor hold or failure to dope the wind will, but a difference nonetheless.
That's what I find interesting about it this match. You have what you're given and it's up to you to make it work when it needs to. Some of the matches that I've witnessed had more in common with benchrest than actual practical marksmanship. This method seems to go in the other direction. I like that, but I still think that a certain amount of luck would be involved. If Shooter A and Shooter B are equally skilled, but Shooter B's rifle shoots 2 clicks to the left and the wind is picking up when it's his turn on the line, he will indeed need to be lucky to keep up with Shooter A. Just my opinion.
I agree with your first statement entirely, though. If Shooter A can't shoot in the first place it really won't make a difference anyway.