Tim,
I just ran a test on my SME V5 server, and created a few i-bays. Not sure about ESSG 4.1.2, but in V5 if you setup you i-bay with the 2 settings below - you shouldn't get the cgi/files/html folders.
==============================================
Public access via web or anonymous ftp: None
Execution of dynamic content (CGI, PHP, SSI): disabled
================================================
Hope this helps. If not I know how to create "custom" i-bays. Let us know.
Regards,
Patrick