For the past 2 years me and my professor have been trying to crack the code on the trifecta of codecs to use with qlab content. 1. Transparency 2. Good quality 3. Reasonable file size.
While the formula I've settled on does compromise on a few of these, I've used it several times in my current show and it's performed admirably. The trick is lowering the image quality inside After Effects since MPEG STREAMCLIP WILL NOT LET YOU REMDER ANYTHING AND KEEP ITS TRANSPARENCY. My custom setting is as follows: QuickTime codec: ProRess 444, quality at 65%. Then make sure you have image + alpha selected, millions of colors+.
This will render and export your content staggeringly fast, and will keep your transparency, and has no visible drop in quality however, this technique is only really effective for animations under at most, 30 seconds. Anything longer and your file size will be massive and likely stutter. My trick has been to render stuff in chunks so anytime there's a pause in the video I can switch it out with another file. Doing this you can stack several images on each other with little concern.
Your only other concern may be getting ProRes 444. I found out I had it by accident when testing different codecs but I realized it came from my old copy of Final Cut Pro 7. If possible find a friend who either used to have the software, or still does and you can likely find the codec buried somewhere within.
Hope this helps shoul anyone in need stumble across this blog!