Since not too many have been able to get a PCV let alone had a chance to play/tune with one, I hesitate to comment on whether it will unleash the 7% power reduction built into the R3. But I would assume that it does no more than a PCIII, and only allows for changes to the injector timing/duration. It probably will not change things like speed limiters and secondary throttle plate position.
If my assumption is correct, you will still need a GiPro and remove the secondary throttle plates to get all the available power in the first three gears. Since the Roadster already has a gear position indicator, it may not be in ones best interest to install a GiPro or remove the plates. Personally I would still do it that way just for the ease of tuning the bike since not many shops deal with TuneBoy or TuneECM. But I'm told that you can do all that with Tuneboy or TuneECM if you have the know how to make tuning adjustments yourself. It's a path you have to choose and stick with, I like the Power Commander just because it was very simple to tune my PCIII, GiPro, Triples and TOR's. I'm more than happy with the overall results.