Well, motoman doesn't offer to cover any warranty repairs, right? Yamaha does, if you follow break-in recommendations. So you should take motoman's advice with a grain of salt. Full disclosure: I'm breaking mine in roughly because I happen to think that machines perform best under load. As long as that load is introduced gradually.
Here's the reason why I think so: It's a matter of cost and brand value. If Yamaha's break-in procedure was inefficient or sub-optimal, it would result in increased maintenance cost and lower brand satisfaction because the engines would incur increase maintenance cost, would not last long and would not perform according to spec. The reason they haven't changed their break-in requirement is because it is designed to get the engine to perform up to stated specs for the useful life of the engine. It's strictly down to total cost of ownership and brand value.
Companies don't simply 'put-together' a break-in process. It's achieved with design sessions with the engineers and mechanics along with quality controls that open and inpect engines adjusting the break-in recommendations to make sure that these recommendations represent the majority of use cases for target geographicl regions operating within tolerance limits - you can tell I'm a corporate suit eh?
That said, I do not believe Yamaha's break-in recommendations are suited to racing and high performance riding at all. I think this is where motoman's claim may have some value.