Thanks for taking a look. We messed with different configurations, and our solution has been to set the bank build directory in FMOD to be the Streaming Assets folder in Unity. Then we point the FMOD config in Unity to those banks as a Single-Platform Build. This appears to mitigate the issues of the banks not being imported/copied over successfully.
Not a perfect solution. But for the purposes of our CI, it suits our needs.
Thanks again.