how do you think it is possible to run a jsfl script when opening a fla file?

Yes, I think it's possible, but it depends on where and how the script that needs to be executed is stored.

Let suppose that you have a convention the JSFL code is stored as a frame comment on layer 1, frame 1 in the main timeline.
You need to have an initialization script installed in the Tools\ folder, which will load when the program starts. In this script, you can use the "documentOpened" event and define a function that, reads and executes the code.
Something like this:

fl.addEventListener( "documentOpened", function(){
	var doc = fl.getDocumentDOM();
	var script = doc.getTimeline().layers[0].frames[0].name;
	var ok = eval( script );
});

yes, with as3 you can use mmexecute().