I have played a little with 3Denlive, and followed the discussion on the 3D Spider-Man.
I am not fully on grips of the application but I feel it is extremely interesting to produce videos out of a sequence of stereo images, including zoom-in/out effects, and overlaying two or more stereo images.
In my opinion 3Denlive as a video editor would work best if the input SBS images are already well aligned for the main angular parameters (visual axis rotation, h-perspective, v-perspective, and nominal focus correction). The only alignment parameter that makes sense for zooming in-out is the h-disparity (displacement in the X direction).
As an example of this take one stereo image that has a 3.3% horizontal disparity. If we make a video sequence that ends in 5x zoom-in, the disparity would become 16.5% which is obviously too much. This is were it makes sense to displace in the X direction trying to reduce the disparity in the zoomed-in area, or possibly masking some area of the image that creates excessive disparity.