Than no problem for you. You may use TM snapshots to set BF and use MIDI from BF in computer. It will go throught USB, not by ADAT.
I do not have AIO and BF, but it should work as in case whan using any RME gear that uses TM. You will be able to swith between BF and AIO and set/recal whatewer you need.
Changing snapshots works independently for each device. But when using ARC USB (maybe other controllers) one may set it so it changes snapshots on several devices.
I use TM to controll four RME devices and no problem. But one driver may controll only up to three devices (I am not sure, if three applies to the same devices or any devices). MyRME devices run on two different drivers, so I cannot test.
The only disadvantage of using USB in this case is the danger of ground loop.... If you attach BF just by ADAT it is electrically isolated from computer.
FF UCX II, Digiface USB, Babyface Pro FS