you do mean the opposite right? Bikes are lean to meet emissions.
No, I mean rich. And I'll give my reason more as a question:
Somebody that has a stock bike (at least as far as tune/intake/exhaust is concerned) - when the exhaust is cool, wipe your finger on the exhaust outlet. Is there soot on your finger now?
If so, that's unburnt fuel that made it to the exhaust, which means a slightly rich tune.
This is done from the factory because the catalyst + AIS will take care of any unburnt fuel (and the ais wouldn't be necessary at all if there weren't unburnt fuel). If it's tuned lean, you're going to wind up with valve and ring damage.
Edit: I do not know the target AFR used by the stock tune for the closed loop area of the stock map. Nor do I know the target values that were used when Yamaha created the open loop map either. When I say that the stock tune is rich, I mean richer than 14.7:1. Adding more fuel will still likely make more power as the extra fuel will allow the burn to be cooler and more controlled.
Edit 2: Since I have a PCV and an auto tune, if I have some free time this weekend I'll load up the stock map again and see what the AFRs are. Granted, I won't be able to see them under load. Most of my experience is with cars rather than bikes. I suppose it's possible that they come lean, but every exhaust I see has soot.
Edit 3: With edit 1 I was trying to say that the stock tune may be rich while still being leaner than max power.