Not sure I understand the concern with TexCoord2/3 … First of all, it is used in the engine, in fact both unshaded and lighting materials use TexCoord2. Its no different than any other attribute.
Consider using a SceneProcessor instead of a Filter. The filtering system is not designed for low-level processing like this.
With a SceneProcessor you can choose to render any mesh you want and do other things which might be required for stereo 3D rendering.
The submit overhead for filters is probably very low … the main performance drain is # of pixels processed by the filter, so I am guessing that both approaches would have similar performance characteristics.
However do note that some filters will not expect the discontinuity in the middle of the screen where the two eyes intersect. For example, bloom, SSAO and possibly other filters do a “blur” like operation, so the left eye pixels will be blurred onto the right eye and vice versa, causing visual artifacts on the sides of each eye.