I just know it always needs readjusting. The same way if you change manifold volume - this always requires rescaling the VE tables too. The MAF won't require much touch up and could be argued that it's just normal skewing, but the VE table seems to always be changed.
It's kinda like putting an intake manifold or heads on something still using the stock intake tube and filter housing - 6500hz should still flow the same air right and thus deliver the same "fuel" right? That's just it though - it doesn't - you usually have to add fuel or take away if you went backwards on the mods and thus increase or reduce - again depending on if you gained or not - the g/s reading. I agree with you. In a perfect world it should be the same no matter what, but I think the OE gets airflow measurements with everything assembled to come up with the original scaling on purpose.
The MAF scaling part was more on the gen3's for whatever reason - typically they leaned out or went pig rich, but small number changes made big number changes for throttle sizing, so possibly played into it there?
Don't know the specifics - just know that's what I've had to do with those changes.
I mean it's kind of like the transients part - all transients are calculated from map and temperature inputs and triggered via rpm changes - if it affects these, it should also effect the base models - right?