The Axis conversion system does not change anything else than the first layer of nodes in the scene, and only their transform. We don't touch vertices and anything like that.
If you need to render in a left hand system, such as DirectX, it is possible to do it without converting any vertice data. The only thing you really need is to set the FrontCounterClockwise to TRUE, and transpose every matrix before sending them to your shader.
Robert Goulet, FBX Dev Lead