I can understand why SOA may prefer to only have one ECU out for reflash - it's cheaper. SOA saves on materials and labor costs, and makes the dealers (some making a good profit on the STi, and others making a killing) fork over the money for loaner cars and warranty service.
If someone was making that much money off of my work product by adding a greasy handshake, smile, and possibly some undercoating, I would expect them to do the same thing. IMHO, the dealers should be forking over the cash to have SOA send them the equipment and software for reflashing the ECU. But hell is still on fire so that won't happen.