The main use case for wrench shortcuts was for processing scripts in the editor.
thus, for scripts which take one arg, a filename, sys.argv is being populated the way you would run from the command line -- [0] is the command name, [1] is the target file. Anyway, that's the rationale behind the first two args -- the idea was to be able to have a script that accepts a file name, and does something to that file -- publishing to a blog, converting markdown to html, etc -- and you could run that script on your desktop or on pythonista in the same way.
Running from the play button or from a home screen shortcut probably shouldn't populate argv[1] unless you asked it to.
Arguably, it would be nice to have a switch in the wrench editor, that says whether it populates argv[1] with the editor filename, or not.
If you want to simulate a pure command line that doesn't pass in the editor filename, you should consider writing a little launcher script, that populates sys.argv, and then calls runpy that way you can run your other scripts. I.e have a single launcher script that accepts as argv the module to run and any argv -- then simply fix argv and call runpy.