Resolution:
The way you can do it is described below:

You just have to give an argument in format like:

       -&ltpropertyName>  &ltpropertyValue>

i.e : -tibco.clientVar.MYTEST yourSubstitionValue

While starting the BW Engine, so for example in attached test case there is a Global Variable 'FromCMD' - so if want to override a default value in designer that is set to 'DesignValue' to something else at run time I just have to do something like

&gtbwengine C:\tibco5\designer\5.1\samples\Global_Var_CMD -tibco.clientVar.FromCMD FromCommandLine

So now Engine will have a modified value of FromCMD in it .

To, test it run the attached Project as shown above and then to trigger it send a tibrv message as :

tibrvsend -test.cmd Test

And, it will show the new value of Global Variable as 'FromCommandLine' - if you don't pass Globla Var value at startup it will print value 'DesigneValue' which is stored in designer.