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I don't know if it still might help, but i've been trying to set the multiposition mode using code as well, and I managed to do it. I've checked the code of AkAmbient.cs (Unity) and I noticed that, before setting the multiposition mode for a gameobject, all components of type "AkGameObj" are removed.
AkGameObj gameObj = soundpoint.gameObject.GetComponents<AkGameObj>();for (int i = 0; i < gameObj.Length; i++) gameObj[i].enabled = false;
I added this portion of code in my soundmanager, before setting the multiposition mode, and now it works :)