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 Alternatively,  i wonder if it's possible to offer support for videos that contain an alpha channel?

perhaps for videos encoded with any of these codecs that offer alpha channel support?
https://pixelbakery.com/recipes/video-image-formats

H.265, VP9 and so on..? 

Might be easier than implementing a second video track :D

I don't think the Quest's hardware decoders support alpha channels, though.

ah that's too bad! :(