Every bike is a couple of clicks away from being the worst handling bike in the world. Obviously a cbr600rr has much more track potential for handling than something like an SV, or a less track orientated bike, but without the right suspension set up, it could ride much worse.
No top racer would ever say the bike rode perfect. It's always a compromise between different factors, stability over turn speed, turn in over braking, etc, so if they say it's perfect they're almost saying they can't improve.
For an answers sake though, to me, the rider sets the bikes limit, so if he can lap 1:40 on a 2003 600rr with 120bhp, he could step onto the same bike with 130bhp and maybe get half a second off the time. He could step onto a 2008 600rr and get another second off though because yeah, like you say, developments in the last few years have been huge and the level has been raised, particularly in chassis development, with much more design in frame stiffness, and rigidity research over various parts of frame and swing arm, crank position, engine position, and with the R1's, fuel tank position, all to aid handling.
You question is answered at every round of WSB and MotoGP when the previous years records are routinely broken, directly because of development. If perfect exists, and was in a time line, it'd be leading, at the very front of the time line, the latest bike, the latest design. Perfect is now, and last year is old.
I can lap faster than bikes from any year, on my 2003 600rr, but that's because I'm not a bad rider, and I'm racing people with more money, hence the better bikes, but not necessarily more skill, so they're not exploiting their bikes improvements over mine. Stick an amazing rider on my bike though and he'll batter my times, then stick him on the newer bike, and he'd probably beat his own times on my bike.
Bongo