Saving out with Alpha channel intact to windows machine? (Motion v3)

I am working with someone who does video on his windows machine using Premier, but I use Motion to add effects to thier video.
They are sending me a wmv version of the video, which I convert into prorez to work on (keeping frame rate and video size intact) and send the video to Motion to add the effects. Once I'm done I turn off the layer with the original video and send back to FCP.
I want to save out a quicktime video from FCP with alpha channel intact so I can send the FX-only layer back to my workmate so he can drop it into his timeline on his machine and have everything align properly.
Any advice on how to do this?

If you have Compressor 4, check and see if you have the Animation codec. If you do, send the Motion project to Compressor and select the Animation codec with the setting 'Million Colors+'. The + (plus) is the transparent setting for the codec.
Open the Motion app and drop the Animation video on top of something to make sure you have the transparency.
Motion has ProRes 4444 that can contain a transparent background. Unfortunately, Windows computers do not support the ProRes codec.
BTW, a transparent background will look black (sometimes white).

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