Ray, the map option in the PC doesn't seem to be known about that much. I certainly didn't know it was there until I went on the Dynojet training they offered a few weeks ago.
There's a few hidden tweaks in there to be had, but the installer just needs to know about them
I've had a look in my map library and there are a few maps in there with individual cylinder maps, but none specifically for the R. 998S is covered with a few though.
The latest USB commanders are really clever pieces of kit. The mapping points have been doubled as well as having the tweaks built in. There's also an ignition module coming out soon that allows rev limit tweaking, as well as curve.