IMO, it would be nice if you offer an option to disable the by default activated visibility in the stage editor, when you load a new file into alias.
For now, every time I load a new file into Alias and keep the old data, I have to open the stage editor and disable the ref-visibility manually.
Maybe you could add a checkbox to choose between Visible ON/OFF in the "Keep-Delete-Cancel" Window to choose the preferred way of the user.
Best,
Arne