I really thought this used to be a feature in CPanel. But you are right, this would be a handy feature, and password protected the directory is one solution, like you said though, its really just putting something out there that just doesn't need to be there.
It looks like the directory information for FTP accounts is stored in:
/etc/vftp/%username%
where %username% is the main username of the account that you are adding the FTP account to.
You should be able to create an FTP account through the FTP account manager, and point it to a dummy folder in your public_html, then edit that file and change that specific FTP account to point to a directory outside of your public_html. You will still need to FTP in as
[email protected], but you should then go to the directory you pointed it to. That directory will need to be created and owned by the main username.
I also won't guarentee that CPanel updates or something else might overwrite this file and "fix" the FTP user, but atleast it gives you something to work with.
Hope this helps.
