Ok, the problems I forsee with the swap are not due to length. Think of the hoodline of the impreza and the fact that the top part of the motor will extend furthur forward where the hood hight is much lower.
Also no automatic I have seen uses a flywheel as there is no need. They use a flex plate which at least on the older subarus was able to switch to a flywheel with no other modifications to the motor.
Personaly I would use a EJ motor in the impreza and leave the H6 to the legacy, outback, and Forester where they have the underhood room to use it effectively.
Also don;t forget that the EJ will ALWAYS have more performace parts avalible for it.