Both tuners mentioned are EFIlive guys, and can flash your trans and engine separately, although it doesn’t make sense to do that independently. The advantage is incremental updating and focus on the one controller at a a time.
The reason you want to do both at the same time is because the operational behaviour of the trans relies on correct torque reporting (from the ECU) to the trans controller.
Physically dealing with torque is the trans controller, modulating torque dumps from the convertor and sometimes commanding input shaft speed from the ECU, clutch pre-fill, apply and release speeds and pressure. So torque management is largely trans controller but still a two way street to the ECU.
I think HP Tuners also recently split its tune files into ECU and TCM following EFIlive also, whereas was part of one “PCM tune” previously.