I did some redaing on the matter and indeed the internal Witchdoctor port is used to connect a Canopus Voodoo(1/2) card directly to a Canopus 2D/3D card. I believe it carries the digital 3D signal to the 2D/3D card's RAMDAC and thus increases signal quality by omitting the analog passthrough.
To use the feature you need both your 2D/3D card and your Voodoo 3D accelerator card to be Canopus brand with the Witchdoctor feature. I would assume you need at least your 2D/3D card to use Canopus drivers. I do not know wether the Voodoo card needst to be using Canopus drivers.
SLI is a different thing allowing you to combine two Voodoo2 3D accelerator cards to create a single image. It used to be that Voodoo2 cards had to be identical or at least very similar to run in SLI mode but 3rd party drivers like FastVoodoo increased SLI compatibility between different cards a lot. Using the FastVoodoo drivers you can probably pair any Voodoo2 with your Canopus Voodoo2 card via the SLI connector. This feature is independent of the Witchdoctor port.
If your question is wether you can use a Canopus Voodoo2 paired with another brand's Voodoo2 using FastVoodoo drivers and still utilise the Witchdoctor port to pass the 3D signal through to your Canopus 2D/3D card I have no idea.
But it seems you already have the cards, so why not give it a shot? Worst case you'll need external passthrough like with any other Voodoo2 solution.
Does this help in any way?