Simple answer, yes.
Why? By "mildly" modifying your engine, you've altered how stuff flows into, explodes, then flows out of it.
But you haven't altered how much fuel and air enter, take advantage of the altered flow, explode and then take the easier exit.
Even just adding a more efficient intake and exhaust exceed the parameters the mothership built into the bikes stock brain and then make it prohibitive to do anything to modify fuel/air and ignition to take advantage of these changes.
In the "old days", you'd pop the carb, grab a handful of different sized orifices (jets) and start swapping until you achieved making it run well. If you were lucky, you gained engine performance.
Power Commanders do all that physical work. We're fortunate that Dynojet provides a unit that is "mapped" (jetted) to our bikes in three steps. Even adding one to a stock engine should improve fueling and ignition curves and result in better performance (think at minimum the curing of the off idle stumble/stall many experience).
The only thing to keep in mind, is that just plugging a unit in (and a couple of the plugs are a total biatch to get to) is not a 100% solution because of manufacturing inconsistencies. But I'll guess it's good start.
Couple things that'll make it better. Spend some time at a
Dynojet tuner shop on one of their dynamometers and with a seasoned tuner. They can make accurate changes to your map to optimize the efficiency of your tune. Again, modern jetting at work.
The other thing and probably more real wordly (and I have no experience with), but takes some time with, is Dynojet's Autotune box. It's an add on to the PC that reads your bikes exhaust at the now unused o2 sensor and alters your map while you ride. From my understanding, you can leave it on and in continuous use, so it constantly makes changes where it feels necessary or save your modified map to the PC and remove the extra box.
So yeah, I think it's worth it.