Finally we choose FFMPEG over HandBrake CLI for our online conversion as FFMPEG can be setup to output multiple videos from a single source. This is quite cool as we can maximise our CPU efficiency. As for previous single bitrate video, we plan to use another server for MBR conversion.
The player will automatically play MBR for any uploaded video from 2nd August 2014. The MBR only worked for Flash HLS and HTM5, not supported for WebM edition yet.