1. Export as H.264 .mov using Compressor
2. Open the file in QuickTime Player
3. Export to MPEG-4 (.mp4) as H.264, and choose pass-through for both video and audio
http://en.wikipedia.org/wiki/QuickTime#Container_benefits
In QuickTime Pro's MPEG-4 Export dialog, an option called "Passthrough" allows a clean export to MP4 without affecting the audio or video streams. One recent discrepancy ushered in by QuickTime 7 is that the MOV file format now supports multichannel audio (used, for example, in the high-definition trailers on Apple's site]), while QuickTime's support for audio in the MP4 container is limited to stereo. Therefore multichannel audio must be re-encoded during MP4 export.
It sure is a bit strange that Compressor does not support exporting H.264 using an .mp4 container. I would recommend sending Apple some feedback about this:
http://www.apple.com/feedback/compressor.html