If you look at our camera setup closely you will notice that the cameras are mounted the wrong way around. When you work sitting at the "open end" of the stand, things nearer to you will end up at the top of the screen - not what you would expect.

But this can be fixed in software: The raspivid options "-hf -vf " will flip the image horizontally and vertically, effectively rotating the image(s) by 180°. But doing so destroys the 3d effect (actually inverses it), one also needs to swap the image for the left and right eye.

Unfortunately the raspivid option "-3dswap" which looks like being exactly the option we want, does not have an effect for us. Instead, we simply swapped out the camera cables at the Raspberry Pi :-) Maybe we should have a look at the raspivid source code and see what's going on there...

Good thing: flipping the images does not add any latency (measured by our Arduino setup), so mounting the cameras the way we did it is perfectly fine.

Another thing we wanted to look into is doing digital zooming. The OV5647 sensor we use has 5M pixels, we are only displaying a FullHD image. So it should be possible to use just a central part of the sensor, archive zooming by doing so, and still don't do any interpolation. raspivid has a promising option for that: "-roi". The documentation says:

Set sensor region of interest
Allows the specification of the area of the sensor to be used as the source for the preview and capture. This is defined as x,y for the top-left corner, and a width and height, with all values in normalised coordinates (0.0 - 1.0). So, to set a ROI at halfway across and down the sensor, and a width and height of a quarter of the sensor, use: 
-roi 0.5,0.5,0.25,0.25    

We want half of the sensor to be used located around the center of the sensor, so the full command line is:

raspivid-3d -3d sbs -dec -hf -vf -fs -t 0 -roi 0.25,0.25,0.5,0.5

This results is a nice 2x zoom, just as intended. Unfortunately, the image is now not as sharp as it was before. I don't think it is due to interpolation going on, but it is hard to tell. It is probably beyond what the optics are capable of. Testing other lenses probably is a good idea. 

[Update 2021-07-16:]  When I talked about digital zooming above, I didn't realize that the camera was running in mode 1 (see 'mode' option in documentation) when operating in FullHD 1920x1080 resolution. In this mode, the camera only uses the central 1920x1080 pixels, already resulting in digital zooming. Zooming further (by region of interest parameters) then of course only does interpolation. Unfortunately the camera cannot deliver 30fps at 1920x1080 using the full sensor. For a un-zoomed full sensor operation, we need to switch the camera to mode 5, resulting in a 1296x730 image that needs to be scaled up for display on a FullHD monitor. But having two modes, an "overview mode" (full FOV at 1296x730) and a "details mode" (partial FOV at 1920x1080, effectively zooming in) sounds like it would work nicely in practice. Having a non-interpolated image is especially important in the details mode, and conveniently it is the case there.