Transparency on stereoscopic renders

Does anyone know how to render stereoscopic images that contain an alpha channel ?
(I have tried but the png and exr images contain black pixels instead of transparency).

If this is not possible, is it possible to render custom depth passes (for use in post production). I have tried to render panoramic images while using a matte material on some models but the material/masks/custom maps are not rendered out in the stereoscopic imagery.

Any ideas ?