Good points. And yes it should show up on paper. But it gets on paper in the first place because there's a theory that tells us to take certain kinds of measurements (glossing over the chicken/egg aspect for the moment).
So, if differences are heard - even if only by some people and only under certain conditions - it may be they are deceived. Equally, it may be the theory is inadequate.
The scientific position is not to ignore data. It's to investigate this data, and build new theory if necessary. Then, we might get something new on paper.
Personally, it does seem to me our current account is inadequate. But this is just speculation. The science way is not to speculate or debate, except for the purpose of hypothesis formation and testing (i.e. experiment).
In my conversations with those who refuse to accept that, for example, the speaker wire from Home Depot can only be the same as the Chord Signatures I had on my ProAcs because of "scientific laws" it's seems that objectivity is not really possible. But that's not a problem if that is remembered and one doesn't become married to their theories. Models and theories can help in communication and sharing of our perceptions but I don't think that it is an absolute exercise. That's fine as that is what living is, dynamic and changing. Those who solidify their ideas will go down kicking and screaming but they will go down.
Measurable objective sound differences may show up in certain test data but you can't be sure what those mean without listening and then comes the subjective models of what is "right".
I really liked that linked quote from Hirsch.
Nice canuck breakdown..