This is actually one I did deliberately.  I added a line to .onLoad() to create a url option.  With the option set, it seemed like having the token argument first made more sense.  It's also possible that I'm the only person in the world that would benefit from this since I don't know many people that use multiple REDCap projects within a single script.  I won't be heartbroken if this gets reversed to its original order though.