The behavior you reported is by design.
We haven't intended that mozc_tool is launched with manually specified options 
from terminal by an end user.
Basically only Mozc code should depend on this kind of knowledge of command 
line flags and ideally an end user can access to Mozc setting dialog from GUI.

Regarding "Preference" button on ibus-setup, you can enable the button by 
adding <setup> section into /usr/share/ibus/component/mozc.xml as follows.

<component>
  <version>1.3.975.102-2</version>
  <name>com.google.IBus.Mozc</name>
  <license>New BSD</license>
  <exec>/usr/lib/ibus-mozc/ibus-engine-mozc --ibus</exec>
  <textdomain>ibus-mozc</textdomain>
  <author>Google Inc.</author>
  <homepage>http://code.google.com/p/mozc/</homepage>
  <description>Mozc Component</description>
<engines>
<engine>
  <rank>80</rank>
  <description>Mozc (Japanese Input Method)</description>
  <language>ja</language>
  <icon>/usr/share/ibus-mozc/product_icon.png</icon>
  <layout>jp</layout>
  <name>mozc-jp</name>
  <longname>Mozc</longname>
  <setup>/usr/lib/mozc/mozc_tool --mode=config_dialog</setup>
</engine>
</engines>
</component>

We are planning to add this section in the next release.

You can also access to the setting dialog via IBus language panel.
See the attached screen shot.
(There are some duplicated items in the language panel as of Mozc 1.3.975.102 
on Ubuntu 12.04; it's a bug introduced by the Debian maintainer.)

Thanks.

If you really want to get some instructions via --help command, please try 
Debug build or unset IGNORE_HELP_FLAG defined in base/flags.cc.
http://code.google.com/p/mozc/source/browse/trunk/src/base/flags.cc#224 

Release build sets this flag. 

Thank you for your replies!

FYI, starting with r124, mozc.xml contains <setup> section.