The afr's that MS see's is solely based upon what it is being told by the wideband controller, doesn't matter if correction is on or not. How they are the same at base altitude and not at altitude makes no sense as again MS sees what it's told. I have seen slight diff between MS and the controller, but that is at all times and is generally due to grounds, if all the settings are correct in MS.
And most "professionals" will know that altitude will make a difference. That is part of the reason O2 sensors are used for.