I've been making good use of rendering After Effects files in Adobe Media Encoder lately (CS6). When it comes to needing alpha channels, it doesn't seem to get the job done.
In the AE encoder, I can do a Quicktime, Animation, RGB+Alpha, Straight (unmatted) color. If I try to do this through AME, I can make it a Quicktime Animation but can't seem to set my RGB+Alpha and Straight (unmatted) settings. Is there another workaround?
When rendering out 50 comps from a project, it's helpful to have it render in the background using AME so I can keep working in After Effects.