So far the only programs that allow this (that I'm aware of anyway) are the old version of QuickTime Pro, and Apple's Compressor. I simply want to add an image sequence to AME, and combine an audio track to that image sequence for export. This would save me an extra step. 80% of my work begins and ends in After Effects. I do very little video editing, so most of my exports are rendered from AE and then exported from Quicktime or Compressor to whatever file my clients request (Most often ProRes for a master version, and h264 or x264 Quicktime files for the web).
Is it possible we might see this feature added anytime soon? Thanks!