Since you can not redistribute a modified version of a non-open source program, most people use launchers. I have a better idea. This may or may not violate lisence, but I dont think it will. What about this. There can be a patch for it. It will only wrk if you have the origional program since it will not host any of it's files in the patch, and it will not violate redistributing copyrights, as the program isn't being redistributed, just a program that modifys it. Would that work? I'd live to see Project 64 portable.
Also, if that doesn't work, can you make a portable version with the author's permision?