I don't have any experience with the water cooled sport bikes (I'm a 70's mechanic...only water cooled bike then was the Suzuki 3cyl water buffalo!!). However, all the recent (past 20 years?) dirt bikes have been water cooled, so I assume the new sport bikes use similar technology, some of you more recent guys can feel free to correct me if I am mistaken.
Basically new water cooled designs now use some form of ceramic spray on liner over the aluminium cylinder (Nickel Silicone Carbide for eg). This stuff is hard as diamond, as basically does NOT wear. This means you now need softer rings. So...breakin now means getting the rings to seat to the hard cylinder liner, which happens much more quickly, but the basics still apply. You need to breakin using sufficient cylilnder pressure to keep the rings pushed into the cylinder wall, so avoid idle and steady throttle, and try to accelerate gently through the gears as much as possible.
The 2nd breakin item is getting the piston when hot, to wear into the cylinder. Because the ceramic liner is so thin, the cylinder and piston basically expand as similar rates (compared to old style iron/steel liners) which means you can have tighter piston to cylinder clearances. So...you need some heat cycles to expand the whole top end so any "high spots" can wear in. Again, on a new water cooled design, this takes less time than on old air cooled engines.
So...for either design;
1. Let it get hot and cool down a bunch of times.
2. Try to accelerate gently, as much as possible, increasing the revs as the mileage accumulates.
3. Change the oil to get rid of the accumulated metal particles.