What should be the final outcome?
Do you want to render a composition as image sequence? Do you want to save a frame from serveral comps with one click?
If the latter, focus on setting a name or renaming the output file with your script.
If nothing works, there is always the Advanced Renamer. This would be a second pass in your workflow, but you can set up AR to get rid off _[#####] quite easy and it's made for batch processing (not sure, but if it has command line, you can invoke it with your script right out of AE).
I finally did it!
At the end I have done it in 3 steps:
1- I run a first script were I setup the Render Queue setting the correct path and the filename.
2- I hit Render
3- I run another script that changes the names of the output files.
This is that 3rd step.
var file = new File (totalFilePath); //path of the file + the fileName.fileExtension
var name = file.name;
file.rename(name.replace("_00000",""));
Thanks for your replies.