With the obvious exception of getting duplicate Sent Items folders (due to the change in what was it 6.5 or 7.x), how does one get duplicate folders in their groupwise client if the POA/gwchecks don't "like" them?

Duplicate Trash, Frequent Contacts, etc.

If duplicate folders causes problems, then wouldn't it be a simple matter of coding the client to simply not allow it?

Just ran into a few users with really messed up email boxes and the deldupfolders didn't fix them at all, we had to manually delete the duplicate folders ourselves.

Sent item I can see, only because the back-end changed one to a system folder (although even then you'd think that for database integrity it would've whacked the existing one instead of leaving it in there).