It is set like this to prevent two domains from creating the same user, the main account doesnt need it because all account names already have to be unique. I do not know of any variables that can change this (although that does sound like a good addition) but you can manually change these names by editting /etc/proftpd.passwd and removing the @domain.com from the username and saving the file. Make sure not to delete anything but the @domain.com because deleting the : that follows will break the passwd file.