Just remember that the ECU is exactly that an "Engine Control Unit".
The engine will not know what ECU you have it plugged into, with the exception of the AVCS solenoids (if any).
So aside from making sure you have proper AVCS control, which is dependent on the ECU and what map is on that ECU, the car (engine) should start and run fine.
The immobilizer array (ign key, ecu, and immobilizer module) will simply not let the engine start if any one of those things is missing or bad or whatever right?
SO, if you run a pre-05 ECU, you should be able to fire that thing right up.
If you are committed to using an Immobilizer set up, I have a complete array from an 05 STI for sale in the for sale forums.
It consists of an ECU, Immobilizer module, Ign switch and matching key all from the same car I dismantled last year.
PM me if you need/want it.