That's not (entirely) how it works. It either lets video through from the passthrough, or its own video, not both. And its own video does not require the presence of passthrough video as a result.
Once the driver activates the card, it internally switches the video from the passthrough VGA to its own output. Meaning that if you used a secondary monitor for just the 3DFX card, that monitor would only show 3D video once the card kicks in, otherwise receiving no signal as it's effectively no longer connected to anything (as the passthrough port is left unpopulated). Some Voodoo cards did it with ICs, others with relays (which would audibly click once the video switched from 2D passthrough to internal 3D, or vice versa).