He likely means that he wants to see "hidden" files in windows explorer, but not as an icon on the desktop. If you choose to hide hidden files, then you cannot see them in the windows explorer. The desktop.ini problem has been solved, but the larger objective of making hidden files visible is defeated.
Is there a way to have Fences not display certain desktop icons?
Perhaps, a special fence area can be defined into which you can drag all the "unwanted" icons (I have 2 desktop.ini icons on my desktop), and then the special fence area can itself be hidden?