well having had a look around I've discovered that Elite is apparently built on top of Mono ( http://www.mono-project.com ),a "Cross platform, open source .NET framework" so it's entirely possible you're correct. I've tried setting the controls in Elite using the inputs from Remote but they're just not being picked up.
Guess I'll have to see if I can find the Mono logs and have a dig about...if what you say is true perhaps I can have Alfred fire a script that simulates the key presses at that lower level, but I have no idea where to start with that one...