samps,
The job of the Power Commander is not to add peak power (that is the job of the can), although it will if the air to fuel ratio is not optimal at full throttle. The job of the Power Commander is to give better driveability, and it will do that even with the stock can.
Check out this bit from the article "Electrickery" in the March 2001 issue of Performance Bikes:
Injection ... delivers a predetermined amount of fuel, according to a 3D map programmed into the CPU.
The map (both fuelling and ignition) supplied with your bike will be a compromise, designed to work across production tolerances, in tune with noise restrictions, emissions and with fuel consumption borne in mind. In most cases, it has to be said, this works bloody well on your out-of-the-showroom superbike.
There may, though, be the well-documented flatspot where the noise regs are measured (4-5000-ish rpm). And although the air/fuel ratio may be very close to the sweet spot, it hasn't been exactly matched to the needs of your individual engine.
Add an aftermarket filter, exhaust system, end-can, or other tuning mods and A/F ratios will be further astray. Contrary to misinformed whisperings, most injected bikes do not self adjust to tuning mods. If you want your injection's fuelling matched exactly to your bike, then this can be achieved using a Power Commander, a load-control dyno and the appropriate software.
If you do not use a custom-mapped Power Commander with the new can, the power will not be as smooth, user-friendly, or fuel-economic as it can be. For best results, use a custom-mapped Power Commander, no matter the exhaust. The engine runs best with the fuel map that meets its individual needs.