Binary limitations. Post-release patches are not made available as jars, so a binary install forces a relatively static implementation that cannot be as readily patched later.
The binary distribution of Sakai provides a shortcut for those that already have Tomcat in place and configured as needed (including the database setup and configuration) and it does so by providing a pre-built Sakai that can simply be dropped into place. All you need to do is unpack the binary archive at the root Tomcat directory and the appropriate *.wars, *.jars, etc., for the Sakai application will be deposited in the correct locations.
The latest Sakai CLE binary archive is available at http://source.sakaiproject.org/release/.