Currently, OOo files are created with directories as specific entries in the ZIP
archive and with extra file attributes stored.  Neither of these is necessary
(empty directories should not be stored, extra file attributes are not needed as
the file is primarily for use in it's archived form) so the options can be
disabled.  Using zip under Linux the arguments needed are:

"-D": Do not add directory entries.  Note that this is NOT the same as not
including hierarchical structure.  Files in directories will have their path
stored and the structure is maintained, but empty directories will not be
created.  This reduces the size of the resultant archive (*.od* or *.sx* file)
and reduces clutter inside of the files, making them easier to work with
manually and closer to the ODF specification which does not for instance require
the Configurations2/ directory.

"-X": eXclude eXtra file attributes.  Don't store user specific file attributes
which are not required by ODF and are pointless when the file is intended for
use as an archive, not for extraction and then access across multiple users. 
Disabling this reduces the size of a ZIP archive and hence an ODF/*.sx* file.