The manual also says something about letting your bike idle for so many seconds after starting before riding during break in.
I do think these motors do need some time to break in.
When i got my bike, i rode it about 500 miles or so the day I bought it. Before I retired for the night in the motel, I filled up the tank and noticed at the station that the bike sounded a lot less clattery than it did when I got it earlier that day, suggesting that the valves settled in.
My dealer was pretty adamant that the oil should be changed at 600 miles (or 500, don't remember), told me that they have seen all kinds of wierd breakin related crap in the oil, so I changed the oil that night, in 33 degree temp.
Another thing to keep in mind is that somewhere between 500 and 1000 miles, those stock tires start to feel pretty crappy!