Hi Mousitsas, You've asked a good question. The answer is a bit involved but I'll do my best not to overcomplicate a fairly complicated subject. Please look at this as a how the PC V works, not as a critique. Like most manufacturers, they don't have an incentive to clearly tell you all the trade-offs.
First, the simple answer. With or without Autotune, the BMS-K has a built-in Barometric Pressure sensor, a built in intake manifold Air Temperature sensor, a built in Battery Voltage sensor. You can disconnect the O2 sensor any time, and the BMS-K will run Open Loop, producing a fuel pulse based on RPM and TPS angle, and also compensate for Barometric Pressure, Air Temperature, Battery Voltage, and engine Oil Temperature during Warm-Up. These compensations are pretty accurate but not perfect. What the BMSK doesn't compensate for is Air Flow (dirty filter), air Humidity, Fuel Pressure or Fuel injector flow rate (slight clogging) or Ethanol Content of the fuel. That's the area that the BMS-K's powerful Closed Loop routines and Adaptation Values really shine. With Closed Loop running, it nails the correct fueling both in the Closed Loop areas ... and in all Open Loop areas ... using its Adaptation Values that it calculates during Closed Loop. (Of course what BMW considers correct is partly mandated by the EPA which is why we want to add fuel. !)
Autotune is a very different beast from the BMS-K's Closed Loop and Adaptation Values. And you can only have one of them at a time. If you connect the PC V with Autotune, you lose Closed Loop. Another factor to consider is, what does the BMS-K do when it can't run its Closed Loop program. The answer is it goes into a sort of Limp Home mode that is never seen on a Dyno run but that occurs while you ride. Here is how a well adapted R1150 would look, notice the AFR spread on the little insert chart, how tightly it holds to 13.8:1:
Here is the same bike with the O2 sensor disconnected. Notice how the Motronic compensates buy running high fuel and low fuel (rather than a straight line) and in the inset chart, how much the AFRs have been spread out.
So the PC V and Autotune get a stream like the one above and then add or subtract fuel to that up/down stream. Note though, under WOT like the Dyno run, the BMS-K is not running the Limp Home pattern and that's why Dyno tuners don't notice it.
Looking at the sample chart from Dynojet below, Autotune works by you filling in a table of AFR targets organized by Throttle Position and RPM (starting with the default table they provide). I've noticed their AFR targets are basic to say the least and not what you would want. (Something important to know is that the BMW designed targets also include a corresponding entry in the Spark Advance and Spark Dwell tables. Since you don't adjust Spark Timing with Autotune, you're pretty much guaranteed to be off the mark with Spark Advance--leading to the potential for pinging at worst or less than the best power.)
So you start with the table of AFR targets. Then there are two modes according to the write-up:
"The Auto Tune kit can be configured to run and correct at all times or by using the "map switch port" on the PCV. You can set it up so that you can switch back and forth between the tuning modes and the base map settings. You can also configure the Auto Tune kit to wait until the bike is at a certain operating temperature before beginning to make adjustments."
Autotune then fills in an adjustment factor when/if you ride your motorcycle under the TPS/RPM combination. You can see that to get a complete tune you have to run in every cell. The best way to use Autotune is "not running all the time" since these programs are know to be imperfect. You need to do some smoothing between adjacent cells quite often. But for the sake of your question, if you do run in correct-at-all-times mode. Then it will adjust over a few hundred miles depending on your riding style. That is much slower than the BMS-K's Adaptation Routines which have short term and long term trims which operate in realtime.
Going back to the issue of how to fill in the table below or whether to use their stock table, the basic AFR target table they ship looks to rich at low power settings and not rich enough at high power settings based on what I've seen.