I think the key issue is weather or not you can put a reference to the user in the subscribe page ID to make it behave like a preferences page. I can imagine sending a mail with links like
https://ethicalpets.hosted.phplist.com/lists/?p=subscribe&id=9&userid=[USERID]
@michiel is this possible? If not I guess I will make a feature request.
This would give phpList admins more control over the whole process without messing with the preferences system. Then I just would not use the [PREFRENCESURL] at all.