I'm not much of a unix geek, so this sort of thing confused me.
The user that made the directory can do a chmod (at least on my server).
Thus if I make a file with PHP I can only easily do a chmod using PHP. I can't change it using my FTP client.
If I make a file or directory using my FTP client, only tne can I do chmod using the FTP client.
PHP on my server appears to have root privileges, so I can change FTP'd files and directories using PHP.
Perhaps something in my experience will get you thinking about your situation.