I was expecting this to remain a problem as I said before in my last post I don't think that the issue was the same so I did some testing.
I have now tested this on 13 machines. I am not able to produce one that defaults to copying visible and not visible alike when autofiltered. I have looked in many options, I have tried to determine if there was possibly a VBA approach that would change an option like this but I am finding nothing. Therefore I am still unaware of any way to change the default. I just know someone out there knows of a way.
Does this happen to your colleague in only this specific book? Or is it absolutely every book he has?
Perhaps my previously posted code assigned to a customized toolbar button would be a temporary band-aid. It would work like the copy button only it would only copy visible cells. Just highlight the range and click the button. If your colleague is a person that perfers keyboard shortcuts to buttons you could assign a keyboard shortcut to the code.