Tested the same Composition with Effects and Animation without the pre-rendered layer Codec Tested with 5 seconds of 9624x1080 Composition in Ae rendering a pre-render layer of Png Sequence it does have Alpha and 10Bit but did not run full tests. on Windows you do need to install the codec (it's free).

MagicYUV - I just finished a project using that codec and the results were amazing.

it can be your best friend if you have a big high resolution project and you want to pre-render certain parts so it won't take forever at the end.

Png Sequence - is great if you need to render bit by bit (you can select 'skip existing files') and it does have 10bit and alpha.

it will give you a very large file size, but if you are in a server based environment (I work also in a news channel) and need to deliver fast without a problem in terms of file size - this is the way to go.

Quicktime Animation will render very fast and it is reliable and popular codec that support alpha with the maximum quality.

DnxHD - heard about it only recently because editors wanted to work with that and to get this codec back - can be 10bit and Alpha - you just need to put the settings right in Ae.Quality Test after: look exact at 400% scanning for noise and Luminance/Color differences Tested with 3:33 minutes of compressed MP4 Video File 2880x2880. this is a comparison table but not taking into account the Alpha. the downsize that it will render the slowest. Quicktime Png - will give you smallest file size and maximum quality + Alpha support - for small sequences that you need to deliver via Web it is the best.what I understand is that the problem is with Quicktime player so a rule of thumb based on advice given here and on other platforms is to install just the basic install of Quicktime with the main components, and not the player, and you will be fine. Quicktime Support on Windows - to my understanding this topic is still in debate with no definite answer from Apple or Adobe.

the ultimate question - how do I get lossless quality and small size and reasonable render time? what to do when I need Alpha? how about 10bit? how can we make a living without Quicktime support? after going back and forth with this for a long time, making comparison tables and consulting with Ae users on different platforms (CreativeCow, AElist, and here), what I have found out is this:

Quicktime alternative for windows