Okay. That works too. But there's no need to guess or research. I have swapped MT and AT ECU's, and done engine/trans swaps.
There's one pin on the car side connector that determines automatic or manual:
*without* that pin the ECU expects and runs as an automatic ECU
*with* the pin, it runs manual
All ECU's are the same, with no automatic or manual distinction, and the ECU adjusts accordingly based on that pin/wiring. The manual trans ECU you buy will be the same ECU as an automatic. The *only* difference is your body side ECU connector has one extra pin "telling" the ECU what it is.
So when you convert an automatic transmission subaru to manual - you swap the transmission and then just address that one pinout, by grounding that one pin - to "tell" the ECU it's now a manual.
It's that simple. And so is buying a manual trans ECU!