The trans module is separate. The ECU can be changed from auto to manual mode by grounding a pin. Look for wiring modifications and perhaps (hopefully) they just unplugged the trans control module. Locked in 3rd gear is what happens when the transmission computer is unplugged.
Subaru, as a general rule, does not use PCM's (powertrain control module) to control both engine and trans. GM has done that since the beginning of the 4L60E, and I think Frod and Chrysler are similar. Japanese stuff tends to have separate modules - which honestly is a pain with the newer stuff since half the problems we see on CANBUS cars are module communication codes. Would be better if they were in one unit.
GD