was explained to my by a factory rep that the break-in period has a lot to do with rings and cylinders. Specifically "seating" the rings to the cylinder. Not for ring seal, however. The wear face of the piston rings are kind of rounded when they're new. The cylinder is obviously "flat", in other words it's not tapered or anything when new. Because the rings are barrel-faced, there is not a lot of contact between the ring face and the cylinder. The piston dissipates combustion heat from the crown of the piston into the rings and from the rings into the cylinder wall, which is cooled by water on the outside. If for some reason the rings aren't seated very well to the cylinder, possibly due to manufacturing tolerances or whatever, the pistons can't dissipate the heat of combustion fast enough to cool the piston tops, which can cause them to run hot. It's more pronounced with 2 stroke engines that have a power stroke every revolution, therefore it's much more important to break them in as the manufacturer specifies (read: ETEC). Lean run, combined with 2 stroke, could be disaster if all doesn't go quite right. 4 stroke isn't such a big deal because at TDC at the end of the exhaust stroke the cylinder is just starting to intake a cool air/fuel mixture which helps cool the piston.
That's how it was explained to me, the easiest way I know to explain it here. HOPEFULLY nobody's confused. Break it in properly. I'm one of those goons who breaks the race car engines in the right way. Fire it up, check for leaks, heat cycle it to 200-220 degrees, shut 'er down and go to the races. From then on, the break in period is wide open full load. Never leaked down more than 5%, never broken or burnt anything up but these are 100% different than outboards. Outboards run at full load, full RPM continually. Cars (well mine) runs full load for 5 seconds and then it's idling. Round trackers run full load for a little while and are on and off the throttle a lot. All 3 totally different from each other and require different types of break in.