The current Poser manual has some information on alphas in video renders:

"AVI movies are rendered in 32-bit color, which by default includes an alpha channel (mask) for each frame. This can aid in compositing the animation with other movie footage. QuickTime movies can also contain an alpha channel if set to render at millions of colors."

It sounds like you have the third party video-editing program access the alpha channel to mask, rather than do anything in Poser (other than render to 32-bit color / millions of colors).

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