I've always broken them in HARD. My break-in includes a push from the showroom or warehouse to the dyno, warmup time and then it's full RPM dynos using the same method that Pat (mototuneusa.com I think) uses.
It's cool as you can watch the power increase with every run as the rings seat more and more. From there, I'll change the oil, do whatever work I intend to do (pipe, gearing, etc etc etc) and hit the track.
After the 1st race day or full practice day, I again change the oil. After 2-3 weekends, it's as broken in as it gets...
Now, to comment on the 'owners manual' methods and possible reasons... If you're NOT racing a bike, you have a LOT of things to consider on breaking in. Bedding in brakes, scrubbing the tires and most importantly, getting used to a NEW BIKE. As a good rule of thumb, I tell street riders on a brand new bike to ride like they're on glass for the first 1000 miles at least. By then, if they haven't crashed it, they will be somewhat used to the bike and can ride harder...