You can choose to link the FMOD Integration to a build folder instead of a project:
https://www.fmod.com/resources/documentation-api?page=content/generated/engine_new_unity/getting_started.html#/
What you can do, if I’m understanding you correctly, is:
- In FMOD Studio, set the build directory to a folder next to the Unity Projects Asset folder.
This way it won’t get included in the game. - In the FMOD Integration settings, change to either Single Platform Build or Multiple Platform Build and point it to the build folder.
- Use relative paths to allow other people to have the same workflow if needed.
Now you have your FMODStudio project separated from the Unity project.