I was very happy to that see that Apple added (back) transparent video support in 6.x,
but I just can't get the proper workflow to create a file that Keynote will read the alpha from.
I usually use After Effects to create & encode the files but I just can't get it to work.
I've tried rendering ProRes 4444 with both straight and pre-multiplied alpha,
and they show up as transparent if I import them again in After Effects,
but they are opaque if dragged into Keynote. I've tried piping them through Compressor
with the same result. I've also tried outputting with the Animation codec to Compressor
and then to 4444, but it just won't work...
I know it CAN be done, because flowtility.com offers transparent ProRes4444 videos,
and Apple actually says it should work. :)