GoneShootin is right on.
I think all here agree that some breaking in process is preferable to none, but which is best is a question that is unanswerable.
I would expect that a barrel shoots its best somewhat early in its lifespan. Otherwise, magazine accuracy tests would be worthless not to mention the arduous process of regulating a double rifle. If a gunmaker regulates a fine double to hit the same point of aim out of both barrels, can breaking in improve this?...no.
Can breaking in help in cleaning?...yes.
The difference is that as internal barrel characteristics change, the consistency in accuracy changes - hopefully for the better. This consistency can be a great advantage for the single barrel target shooter who can adjust his sights to use it to his advantage. I don't think the same can be said of a doublerifle.
Anyway, not many will put that many rounds through a double, so my point may be moot.
As for manufacturers, it is in their best interest to make as accurate a rifle as is possible right out of the box. Some may be marginally better than others, but I would be surprised if there is a statistical difference once a load that barrel "likes" is found.
Which brings up a question for you benchrest guys out there.
How do you commit to a specific load when you buy a new barrel? Do you settle on a load first and then go through your break in process?

Huvius