Keys for cars with immobilizers have three parts: the physical key(which you're not using and is cut off of your fob), the RF remote part and an immobilizer chip.
The physical key activates a conventional switch, so it is not really needed if there is another switch like you have obviously(with it's own key).
The 2009 Legacy has an immobilizer chip which I believe must be in proximity to the receiver which is probably in the dashboard somewhere, along with the entire Subaru cluster(which is how Lawing did his last few cars).
Sorry I can't be of more help, I'm not a Subaru mechanic and never worked for any dealers of any brand.