The "Scripting Options" step of the wizard allows you to change the scripting options. The command line wizard will save only options that are different from the default ones.
The following fragment is an example of the xml generated when some options are changed:
<DataCompareOptions>
<LogScriptExecution>true</LogScriptExecution>
<ScriptExecutionLogFile>D:\QA\xSQL\SqlData\Cmd\Logs\exec.txt</ScriptExecutionLogFile>
<DisableTriggers>false</DisableTriggers>
</DataCompareOptions>