This is exactly what a Power Commander does NOT do.
If you install a PC, you (or whoever does the setup) need to have a specific goal in mind (extra power, improved fuel consumption, rectifying mistakes in the original fuel map, etc.).
Next, you need to obtain (or if necessary, create) a fuelling map that enriches or enleans accordingly, at every single point in the rev range. (And if you've ever had a look at a PC fuel map, you will realise that it doesn't just enrich or enlean according to revs - it does it according to load as well. Engine load is a dynamic factor that is a function of throttle position vs. revs vs. vehicle speed.
This is why most first-timers get the map wrong - they can't visualise the load they put on the engine under most circumstances vs. how their riding style translates into enrichment/enleanment requirements, and then translate that information into the enrichment/enleanment percentages that they need to create or adjust each point on the map.
All this is a long-winded way of saying that the PC does not choose 'the best' fuelling for your bike. It is not 'intelligent'. It can only do what you have told it to do - for better or for worse.
(Like most computers, really).
The Autotune module does not give you an easy way around this issue, either. All it's there for is to remove some of the guesswork by telling you whether the enrichment/enleanment results you have specified are being translated into specific Lambda (exhaust oxygen content) values, and therefore tell you whether your bike is or isn't fuelling according to the map you have specified. If it is, you have the option to accept the values. If, not, you can choose to alter the map and start again.