The Scripting Options step of the wizard allows you to change the scripting options. The Command Line wizard saves only those options that are different from the default.
The following fragment is an example of the xml generated when some scripting options are changed:
<DataCompareOptions>
<DisableSystemVersioning>true</DisableSystemVersioning>
<StretchedTableQueryScope>LocalOnly</StretchedTableQueryScope>
<CompareViews>true</CompareViews>
<LogScriptExecution>true</LogScriptExecution>
<ScriptExecutionLogFile>D:\QA\Idera\SqlData\Cmd\Logs\exec.txt</ScriptExecutionLogFile>
</DataCompareOptions>