I think something benefitual to those using UGCC for both Administrators and those who are selling servers, would to hide all files with chmod -x, as this would allow us to protect private information, such as database information, and protect files such as srcds_run, and those of the similar you wouldn't want to have edited/touched.
This way, only those with SSH to the server box can view some files.
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A second option, to add with the first, is to add filtering. You can list file-paths/names to hide from FTP view to everyone except "god" admins.
Hope these make sense, would love to hear what others think.