This is a big consideration with respect to the 1199. The ride by wire and integration of the electronic controls for traction control, engine braking control and even possibly the quick shift all mean changing fueling to improve engine performance can potentially negatively impact other features of the bike. In the 1199 there is integration of fuel management and power production with other systems and controls.
At least one tuner has gone to the extent of sawing open an ECU and connecting a test harness to the processor to try to reverse engineer the firmware so the interaction of the 70+ tables which the ECU has can be understood.
No one has a problem uploading a map. The problem is understanding which tables out of the 70+ should be changed and what the values should be changed to. For example, there are tables for fueling in each gear for each cylinder, there is a table which controls overall fueling, and there is a table which controls throttle progressivity. There are accelerometers used to discern acceleration, deceleration, lean and chassis attitude. Without understanding the interdependence and interaction between the tables and values, there is significant risk of making changes that make some things better while making somethings worse. Lastly, of course while tuners can test power output, there is no test for ensuring traction control or ABS works when leaned over on the power, on the brakes or when the rear wheel is sliding, the front wheel is pushing or both are happening.
I've heard that the factory supported superstock teams have 10 more hp than the non-factory teams running the stock ECU or a Motec ECU due to their inability to get as good a tune. Personally, I can't see how a traditional band aid tuning solution like a Power Commander stands a chance of working properly.