Non-unique file names do get flagged as non-unique in the Compare Status column of the workspace, but not all of them do. If the conflicting item has been uploaded, thus reserving the file name, but has not been checked in, it does not trigger a flag in another user's workspace. It will, however, prevent check in for that other user, with the error that it is not unique.
PTC has accepted this as correct behavior.
Consistency is key. If the file name or number is non-unique, it must be flagged in the Compare Status column of the workspace, no exceptions.
Also, no, we aren't going to use the preference to allow uploading non-unique file names, because it doesn't actually allow uploading non-unique file names. It really just renames the item to a unique file name, but it causes more problems than it solves.