But a small stub exe isn't a reliable way as when EnigmaVB launch the exe inside the box, it have to create a random stub exe, which can be stopped by AntiVirus as possible heuristic threat.
I've seen that already, Microsoft Security Essentials asked me if I would like to submit the boxed exe for ...

Would it be possible to have some sort of symbolic link of "input file" to "%DEFAULT FOLDER%"?

I am trying to pack node-webkit application with native module. For this to work, boxed application also needs to be named nw.exe - which I would like to avoid.

https://github.com/rogerwang/node-webkit ...