Software to re-encode 3D video into the original 3D format, but lower bit rate?

[RasterEyes]

I can pass H.264 3D video (described by MKVToolNix as "both eyes laced in one block (left first)") into Handbrake, and it doesn't choke on it, but it just handles is like regular 2D video and outputs 2D video. (I think this 3D format is also called "frame packed".)

Of course, if I had a 3D source material like side-by-side or top/bottom, Handbrake would handle it just fine, but (1) I have yet to see a commercial Blu-Ray in such a format, and (2) such formats are far less efficient, going in the wrong direction for reducing file size.

For now, I'm just ripping 3D videos to MKV without any re-encoding*. My Zidoo handles these files just fine. Since I don't own that many 3D Blu-rays, it's not like the extra disk storage space is a big deal, but it does mean streaming these videos requires a bit of extra network bandwidth.

I'm also using MKVToolNix to re-add features to 3D videos, and 4K videos for that matter, such as commentary tracks which are often only on the standard 2D HD Blu-ray.

*Interesting side note: If you rip a 3D video using MakeMKV, by default the video track is unchecked, and must be explicitly selected to be copied.