Santo,
yes, it is possible. In fact, the current version of the MOD has compatibility with Quadro videocards (nVIDIA) which have direct absolutely parallel two buffer channels, and in that case it produces two full images but in different buffers for the left and the right channels. Then the video card mixes them to your convenience.
It is completely possible to do what you request, but there are some considerations.
Any video codec will process the frame sequence trying to set what typically are called "key frames", it means reference frames that they take as base and they save full detailed and later, a sequence of updates (only by zones and details) that are "corrections" to the key frame with the updated zones, but avoiding retransmitting full frames. As you could imagine, if you try to alternate frame by frame the images corresponding to left / right eyes, the image "seen" by the codec, will have differences big enough as possibly avoiding it from finding key frames and subsequent updates. If so probably the codec would not be able to compress video, or at least will have to cope with important problems.
That's why many times you see that videos are generated in the side by side image (one channel in a horizontally narrowed frame to the left and the other to the right). But in this way, the two channels never update bubstancially (because any region of the screen never has too many changes from frame to frame).
I really don't know much about recent video capture software, perhaps something has been developed to work with these day to day more frequent problems.
The full framed full color left / right alternance can be perfectly implemented, and without much trouble. But I don't know how can it be taped efficiently let's say. The other eventual problem is if sometime your fps counter gets low. With anaglyph you still are safe, because you have a full image (red / cyan or whatever) always. In the other system you can see important flickering when the fps count is low.
Regards,
Pablo