I do believe there will be some flexibility in this -- I am trying to figure out just what limitations the actual server side encoder has at this point because I know from my experience that I can most likely do some scripting magic to demux the audio and video prior to server encoding into Divx format incase it has problems. I have to see how the server-encoder responds to the different formats.
I remember that when I tried to upload, it basically rejected anything I sent to it unless I had it in Divx format before it even hit the uploader (at Stage6). I think I can setup something that examines the video and audio streams, demuxes them if they're in an odd format, and encodes them into acceptable format for the server-encoder and re-mux before the encoder gets the upload from the client.
I'm glad you brought this up because I had actually spaced out on that problem with the other site --