As far as I can tell, if I want my quicktime to have an alpha embedded, it has to be animation or PNG codec?
That's fine, but I need the file size to be as small as possible, and I'm having trouble compressing these down to miniscule proportions. I'm use to compressing via quicktime pro at H264 which does a magnificent job (as in turning 500 MB into 5), but I don't want to lose the alpha.
One workaround is to render the clip in H264 and then render a separate alpha/matte pass using the same- of course that implies that you can use the two on the other end. If you need an embedded alpha Apple ProRes 444 should give you smaller files than Animation.
As far as I can tell, the 3 codecs that retain alpha in a quicktime are animation, PNG, and prores 4444. But they all do a terrible job of compressing. You lose the ability to clamp bit rate, and only animation gives you a quality slider that doesn't do a very good of compression (even with it cranked down to zero) while looking terrible.
It sounds like it's just impossible to get great compression with the an alpha channel in a quicktime.