The local avoidance core system is completely separate from the Unity stuff (like transforms and GameObject's), so the only thing which actually assumes the XZ plane is the RVOController. There is no out of the box solution, but I think it should be relatively easy to modify it slightly so that instead of using the X and Z coordinates which it passes to the Agent, you use the X and Y coordinates. So for example in the Move function you would set the desired velocity to
desiredVelocity = new Vector3 (vel.x, 0, vel.y);
to trick the internal scripts that the Y coordinate is actually the Z coordinate.