I've beaten every bike right from the second I pulled it off the showroom floor. Made a point of coasting the motor down from a hard run through 4th gear within the first 25 miles of every one of my bikes. This is what engine builders do to their engines, they supposedly don't last as long but who is going to keep their sport bike for 50,000 miles or more anyway? Few, I think.
All of them have run great. Test them for compression after 10,000 miles and they're usually above factory spec because I got the rings seated in good right from the start. My 2003 GSX-R pulled 154whp with 23,000 miles on it and no mods, compared to the dyno shop owner's bike at 141whp and 11,000 - he was floored.
Now with 5,000km on my Tuono, I did a run against my friend's RC-51 yesterday. Despite outweighing him by 60 pounds and him having a fairing (and a few modifications), the Tuono stayed right beside him to 245km/h and eventually lost by a bike length at an indicated 255. Now that, gentlemen, is a good strong Tuono. The fairing and weight difference would have seen him humiliating me if we'd switched bikes.
So my advice is, break it in like you mean it... don't do a lot of hard throttle in high gears, stick to lower gears for hard acceleration and try not to chop the throttle on and off in large amounts for a thousand kilometers. The first few times you rev it hard, let it coast down without brakes or clutch. It'll be just fine and it will work better for it.
Or break it in like the manual says and maybe it will idle a little smoother. Engines do that with lower compression.