If I understood you correctly...
Every system users can be FTP users, but every FTP users cannot be system users.
If you assinged a permission to a directory/file for a system user, that user can use it depend on this permission when he/she accessed it via FTP.
If you have only FTP users (the user in 'ftp' group only, not system user), you can set the permissions for 'ftp' users. And this permission will be affected on all only FTP users.
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