Best visually lossless codec for cartoon prerenders with alpha

Hey guys. I've done a lot of research on this but still cannot find a satisfying solution.
I have hundreds of comps that I would like to prerender and re-use on a regular basis. These comps are simple solid colors, cartoons, for character animation. They contain LOTS of blank space, with the image only comprising a small part of the frame. This is necessary to line everything up in the end. I need to be able to decode these prerenders on Mac and Windows, but it is OK if they can only be encoded on Mac. I need it to be a fast codec for decoding, but I do not care how long it takes to encode them. I don't care what the container is, but Quicktime seems like the best container that AE supports.
After doing lots of tests, the only reasonable formats I could find were:
ProRes 4444
Animation
I have tried DnxHD, PNG (Quicktime), PNG (Image sequence), and all the other ProRes variants (with a separate movie for alpha). DnxHD doesn't work because it only works at fixed sizes and maxes out at 1920x1080. All the other ProRes variants don't work because they don't have alpha, and when I use a separate ProRes render for Alpha, there's artifacts on the edges. PNG in quicktime is far too slow to decode, and the files are bigger than Animation. Using image sequences is a pain to maintain and seems to be slower as well. I wish I could try out codecs like HuffYuv and Lagarith, but they are not supported on Mac.
ProRes 4x4 would be perfect, but I have no need for 16-bit color. Animation is the fastest codec, but produces files that are too big. At 75% quality, it produces files smaller than ProRes, but introduces some artifacts.
Wondering if there is an 8-bit codec with alpha that anyone would recommend for this.
Also, I am wondering if using a single, very long Quicktime file is faster for AE to use than lots of shorter Quicktime files.
Thanks,
Bryan

I think I found that PNG was kindof slow to render. I will give it another look.
The duration of the file question is really just about how AE manages its memory. Whether having a single file is better or many files. For game development, I am used to generating single spritesheets which contain all image data, rather than many small files. I am wondering if something similar is true with AE. I am basically trying to optimize our workflow as much as possible for maximum AE performance.
In the case of using one quicktime, it would be duplicated many times in AE, and time-remapped to break it apart into layers. Or it would simply already be broken apart as separate files. All files would be used all the time, as they are all the elements of a character's head rig (eyes, eyebrows, mouth, etc). In case you are wondering, the reason I want to prerender them is because they contain a lot of CPU-intensive effects (Mesh Warp, etc). These head rigs really slow down our workflow and also cause frequent crashes.

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