For doing the privacy glass- should I be doing a double StretchRect operation there? It seems like I ought to be following the basic DrawIndexedPrimitive approach as a matter of architectural purity.
Your instinct for "architectural purity" is leading you directly to the final, ultimate tier of stereoscopic modding: Stereoizing Render Targets.
If you want the room behind the privacy glass to be in true 3D, you are absolutely right—you must perform a double StretchRect.
However, there is a massive logical trap here. You cannot just do a double StretchRect into the game's original destination texture, or the Right Eye will overwrite the Left Eye!