Speed density systems use a programmed set of variables to deliver the fuel requirements of the engine. It reads things like engine temp, throttle position, 02 sensor, etc and delivers a set fuel curve.
Being the animal it is it doesn't look to me like it would be able to adjust much.
If the Power Commander eliminates the o2's (I don't mean remove them) then the only way I can see that it works is to increase the hold time on the injectors. If it does only that then the rest of the variables such as engine temp and throttle position is ignored. At least I would think.
Right now I'm thinking I would rather take my chances with leaving the speed density system to do it's thing.
At this point I doubt if Yamaha knows or any body else. If the FI bikes start coming in with failed valves and pistons at 40-50-60 thousand miles, then we'll know. IMHO