No that is not correct. If you want to
apply/submit an application after the 30 September you have to pay a late fee as September 30 is the closing date for submitting on time applications.
But if you have already submitted an application and wish to change your preferencces after 30 September, you can change them at any time until the cutoff date for the main round (Wed 7 January 2009) and it will not cost you (i.e. UAC does not charge you to change preferences).
To confirm this please refer to the UAC website, such as the
FAQ here which states that they do not charge you to change your preferences.