I don't know the details about the Power Commander, but my tuner told me that with the SE Pro Race Tuner that he gets more data points to work with and that he can adjust the front and rear cylinders separately.
That does NOT mean you cannot with the PC, I'm just telling you what I was told about the SEPRT. As previously stated, I don't know what he PC can do. My '11 Limited is tuned with the SEPRT.
Iron Butt Association Member #46654
'11 FLHTK - Ultra Limited (Black Betty)
SE Stage 1 A/C, SE-255 cams, SE Pro Race Tuner HP: 85 TQ: 102
'90 FLHTCU - Ultra Classic (Phoenix)
Paughco Rigid Bobber Project (Diamond)