Another reason why some shops will tell you this, is sort of a mental thing that'll cause you to ride with more caution/more relaxed than if they were to tell you to go right ahead and ride it like you would every other day. As much as they want to sell you something/add on to that sale someday, they don't want to see you wreck the bike right out of the lot -- it's to protect both the rider and the bike, as well as their own liability.
While I agree that the manufacturer-recommended break-in procedures are a bit conservative, I suspect that they too are partly an effort to prevent a new rider (or rider on a new bike) from getting in over their head and crashing the bike by riding beyond their immediate capabilities with it.
Think of it this way: You upgrade from a Ninja 250R, which will easily rev up to 10k without much fuss and without overpowering acceleration, to a bike like a CBR600RR or an R6, where revving to the same extent might send you careening out of control. But with the "break-in" period mentality, you'll be accelerating more cautiously and cornering less aggressively etc, which will in the end help you learn the power band and handling differences of your new vehicle.
Smart if you ask me, though really it should be common sense to at least take it easy while you learn the ins and outs.