You're making the false assumption that users only use the "raw command line" for entering SITE commands. If someone wanted to enter "SIZE file-name.zip" to retrieve the file size of a certain file, FlashFXP would then interpret it as "SITE SIZE file-name.zip".
The
SIZE command is an FTP command supported by most servers and the
SITE SIZE command is supported by fewer servers. In this scenario, how is FlashFXP supposed to know when to prefix the command with SITE and when not to?