The usual power-commander tinkering I would describe more as "calibration" rather than "tuning" but even with that, it can range from simple to complex, and there are right and wrong things to do.
What usually happens is that someone finds/downloads/whatever a map for your bike that most closely matches your configuration, plonks that into the power commander, maybe does a dyno test before and after, and as often as not, calls it good. Pluses: cheep, fast to do, no waiting, people can afford it. Minuses: you are subject to the whims of whoever originally made up that map and whether they did it right or wrong. If the map was done PROPERLY and the configuration is somewhere near what you have, this is the best bang for the buck for most people.
The next most common thing is that you go to a dyno tuning place that has what is called "tuning-link" and exhaust gas analysis. In one full throttle dyno pull it measures the exhaust gas and makes a corrected map and that gets downloaded. The good: cheep, fast to do. The bad: doesn't do a THING about part-throttle operation (or if they do it, it often happens wrongly - more later), and often the results are sub-optimal because this is being done on an inertial dyno. There is a time lag between certain operating conditions existing, and the reaction of the exhaust gas analysis equipment. I know this is what Dynojet has, but it's not really the right thing to be doing.
The problem is that "real" EFI calibration is something that most people are not willing to pay for. You do it on a load-control (water-brake) dyno. You establish certain conditions (e.g. a certain throttle position and a certain RPM) and then you vary fuel delivery to get it in the ballpark, then you vary ignition timing to get the highest torque reading, then you vary fuel delivery again to confirm it, etc. You do this over the full map - e.g. every combination of throttle position and RPM. Needless to say, this can take quite a while!
Then there is another complicating factor that most "tuners" don't consider.
At wide-open throttle, it's obvious that the rider wants maximum power (i.e. maximum torque output at that RPM). The optimum ignition timing coincides with this objective. The output torque is easy to measure. This is not a problem.
The big problem, and which most "tuners" don't get right, is the part-throttle operation. At part throttle, the rider is not asking and does not want maximum possible torque output. What's actually wanted in those conditions, is smooth throttle response and minimum fuel consumption (at an OEM level, emission considerations overrule this but aren't completely inconsistent with those objectives). Brake specific fuel consumption is harder to measure, because at a given RPM and throttle setting you have to measure both the output torque and the fuel consumption. On a fuel injected engine, you can infer fuel consumption from injector pulse duration.
Anyone who tells you that they are looking for a set air/fuel ratio over the full RPM and load map, is doing it wrong. It will frequently be found that full throttle wants to be set to the maximum-power ratio (with gasoline, frequently air/fuel 13:1 give or take) but at part throttle, best BSFC and driveability will frequently be on the lean side (15.5:1 - 17:1). And no, you will NOT burn a valve or piston by doing this as long as you stay clear of detonation - which doesn't happen as much at part load anyway. The heat load on the pistons and valves is lower at less than full load, so there's nothing wrong with going lean in that range (and it will be easier on your wallet, and won't foul spark plugs, and won't carbon up rings, and won't wash oil off cylinder walls the way a too-rich setting will.)
I've only done full recalibration jobs on a carbureted engine with the assistance of a wide-band air/fuel ratio gauge - in my case, I did my track bike Yamaha FZR400, and it worked out so well that I did my spare bike, same model but street registered. Full throttle is 13:1 give or take, and on the street bike I managed to achieve slightly lean of stoichiometric (15:1 to 17.5:1) over the full range of cruising conditions from 40 to 120 km/h. Throttle response is better than it has ever been, and fuel consumption was cut from 6 L/100 km to 4.4 L/100 km. It's got a little lean stumble at moderate load while the engine is warming up, but after it has been running for a couple of minutes, it's perfect.
The combination of settings required to achieve this was something I would have never hit without the gauge in hand. Pilot jets are actually richer than stock, idle screws a little leaner to compensate, but this allowed the needles to be one groove leaner than was possible with the stock pilot jets. Main jets are one size leaner than stock on the track bike and stock on the street bike (the setups are not identical - the track bike has different camshafts). Richer is not always better, that's for sure.
Helibars, MRA screen, Ohlins damper, reversed shift pattern, sorted suspension, braided lines, Michelin Pilot Power, all else stock 'coz it's fast enough!