Yes PCV will only affect fueling AFTER the ECU has done it's thing.
PCV monitors the Throttle Position Sensor, I think the Fly By wire servo motors still provide the exact same % throttle in either T or S... it is just that the rotation ramp up of the throttle is faster in S mode. This can be tested by hooking up the computer the the PCV and watching the throttle % value change in S and T modes - ignition on but engine does not have to be running to moniter TPS.
PCV does Not replace the ECU fuel mappings. The PCV fuel maps are just small + or - values or 'correction' on top of the ECU fuel mappings.
You can always load a ZERO fuel map into the PCV and it will run only ECU values.
Now that being said and I could be wrong here for the S10...
1) I think I read that there are a few fuel maps in the ECU... I can only assume that S and T modes have slightly differing Fuel Maps, S mode is so much more aggressive and the induction noise is far louder in S mode, so there is definitely something going on other than fueling - butterflies opening up earlier? etc.
2) how does the PCV manage these 2 modes then if there are actually 2 fuel maps for T and S modes.... well that is where I think the Autotune 200/300 comes in. You set a good base PCV fuel map, then let Autotune EFR map manage fuel trimming on the fly. You will always have fueling automagically mapped to EFR values - eg weather changes, and altitude.
So does this work with aftermarket ECU flashes... YES (but you base PCV map will need tweeking or just let Autotune adjust it to EFR values
)
So my theory above with using Autotune is that the T and S modes should not be affected by the PCV/Autotunes etup at all - or should I say the PCV/Autotune should not notice difference in S or T modes or what ECU flash you run.
My PCV knowledge come from me playing with my PCV/Autotune 200 setup on my 2012 Kawasaki Versys 650.