Firstly, thank everyone for viewing this question.
My question is, can we ceate an Adobe After Effect project (*.aep) in a way that it can run a script on startup if it is called from aerender.exe.
In short, the flow is :
1) calling aerender.exe, passing parameters to specify output video (as flv)
2) when the project is opened by aerender.exe, it must run a script from a *.jsx file FIRST
3) after the script is complete, we move to the render stage.
Best regards.