The guy at the mototune thing really is not an engineer and has no data to back up any of his theory... Not saying he is right or wrong, just not the guy that was paid 6 figures to design a motor and make it last. The factory has a vested interest in your bike for the first year.. they have to warranty it, and they would like you happy enough to buy a new one when you are done with this one...
This picture he has is rubbish.. Find me a builder that will say both these pistons have a full season of racing on them and they came out of the motor looking just like this...
Things have changed over the years with all new engines.. 20 years ago motors were assembled with different materials and methods.. As engines evolve so does the assembly. I think the "run in" has more to do with the drive train now days than the actual motor..
As the material of the rings changed, a lot of other stuff did to. Chromoly rings took us a bit by surprise when they came out.
The final hone finish was something we often did and was a simple 45 degree crosshatch.. This wiped out a brand new set of chromoly rings in about 10 minutes.. There were stories about "how long it took to seat chrome rings" fact was, they seated and wore out in minutes..
I took a boroscope down the top of a new bike motor and the cylinder walls look polished. Not much run in needed there
But there are a lot of other moving parts that do need to get to know each other.. I would follow the factory suggestion myself..
And then there are the "well race motors get broke in at WFO" yea well we also build them worn out already with the exception of the piston/cylinder wall clearances..
There is lots more to this but the debate will go round and round forever..