This is where we'll have to agree to disagree.
I was referring to what you wrote about "why would there be different profiles for eg. strats and les pauls in commercial packs". I can assure you that those are there because the reference amp was tweaked to those, not because the profiles were refined with those particular guitars at identical amp settings. That would be ridiculous - if you go through the hassle of creating a new set of profiles, why not tweak the reference amp, even just slightly, to better fit that guitar??
Without a test (or the designer to weigh in) I suspect Z may very well be discernable. Yes, the KPA will reproduce something, but is it the same something a tube amp would produce once the guitar is changed?
The designers HAVE weighed in on very numerous occasions. There is no reason to speculate much beyond that.
While it is within the realm of possibility that the refinement step may yield very slightly different results, I think we would be talking miniscule differences. What about other nuances? where you pick the string? Which pick? which pickup position? how high output from the pickups? which pickup height? Pickup brand?
Either the refinement process works as close to perfectly as is possible, or there is a difference but with way too many variables to ever do anything about. The only thing that matters is that the person doing the profile makes sure that the profile is identical to the reference amp in sound, and does a through playthrough.
All this talk is just a red herring. Are you asking because you have experienced a deficiency, or because you have surmised that there must be one???