I dont know if I understand your question properly, but anyways in the default bootstrapper this is how we pass the arguments from command line:
<Wix>
<Bundle>
<Variable Name="CommandLineArgument" bal:Overridable="yes"/>
<Chain>
<MsiPackage>
<MsiProperty Name="CommandLineArgument" Value="[CommandLineArgument]"/>
</MsiPackage>
</Chain>
</Bundle>
</Wix>
Make a note of the BAL:Overridable. That's how I was able to make sure that we can pass the property value from command line.